STU 3 Candidate

This page is part of the FHIR Specification (v1.4.0: STU 3 Ballot 3). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions

4.37.10.2 StructureDefinition: Consensus-sequence-block

The official URL for this profile is: 

http://hl7.org/fhir/StructureDefinition/consensus-sequence-block

Describes consensus sequence block used in HLA typing report

This profile was published on Fri, Sep 11, 2015 00:00+1000 as a draft by Health Level Seven International (Clinical Genomics).

4.37.10.2.1 Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots, and how the XML and JSON presentations work.

NameFlagsCard.TypeDescription & Constraintsdoco
.. Sequence ∑0..*SequenceA Sequence
... meta ∑0..1MetaMetadata about the resource
... implicitRules ?! ∑0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: IETF BCP-47 (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... sequence-consensus-sequence-blockPhaseSet 0..1integerPhase Set
URL: http://hl7.org/fhir/StructureDefinition/sequence-consensus-sequence-blockPhaseSet
... sequence-consensus-sequence-blockExpectedCopyNumber 0..1integerExpected Copy Number
URL: http://hl7.org/fhir/StructureDefinition/sequence-consensus-sequence-blockExpectedCopyNumber
... sequence-consensus-sequence-blockContinuity 0..1booleanContinuity
URL: http://hl7.org/fhir/StructureDefinition/sequence-consensus-sequence-blockContinuity
... sequence-consensus-sequence-blockStrand 0..1integerStrand
URL: http://hl7.org/fhir/StructureDefinition/sequence-consensus-sequence-blockStrand
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... type ∑1..1codeAA | DNA | RNA
Binding: sequenceType (example)
... patient ∑0..1Reference(Patient)Who and/or what this is about
... specimen ∑0..1Reference(Specimen)Specimen used for sequencing
... device ∑0..1Reference(Device)The method for sequencing
... quantity ∑0..1QuantityQuantity of the sequence
... species ∑0..1CodeableConceptSupporting tests of human, viruses, and bacteria
Binding: SNOMED CT Codes for species (example)
... referenceSeq ∑0..*BackboneElementReference sequence
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
.... chromosome ∑0..1CodeableConceptThe chromosome containing the genetic finding
Binding: chromosome-human (example)
.... genomeBuild ∑0..1stringThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
.... referenceSeqId ∑1..1CodeableConceptReference identifier
Binding: ENSEMBL (example)
.... referenceSeqPointer ∑0..1Reference(Sequence)A Pointer to another Sequence entity as refence sequence
.... referenceSeqString ∑0..1stringA Reference Sequence string
.... windowStart ∑1..1integer0-based start position (inclusive) of the window on the reference sequence
.... windowEnd ∑1..1integer0-based end position (exclusive) of the window on the reference sequence
... variation ∑0..1BackboneElementVariation info in this sequence
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
.... start ∑0..1integer0-based start position (inclusive) of the variation on the reference sequence
.... end ∑0..1integer0-based end position (exclusive) of the variation on the reference sequence
.... observedAllele ∑0..1stringNucleotide(s)/amino acids from start position to stop position of observed variation
.... referenceAllele ∑0..1stringNucleotide(s)/amino acids from start position to stop position of reference variation
.... cigar ∑0..1stringExtended CIGAR string for aligning the sequence with reference bases
... quality ∑0..*BackboneElementSequence Quality
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
.... start ∑0..1integer0-based start position (inclusive) of the sequence
.... end ∑0..1integer0-based end position (exclusive) of the sequence
.... score ∑0..1QuantityQuality score
.... method ∑0..1stringMethod for quality
... allelicState ∑0..1CodeableConceptThe level of occurrence of a single DNA Sequence Variation within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
Binding: LOINC 53034-5 answerlist (example)
... allelicFrequency ∑0..1decimalAllele frequencies
... copyNumberEvent ∑0..1CodeableConceptCopy Number Event: Values: amplificaiton / deletion / LOH
Binding: CopyNumberEvent (example)
... readCoverage ∑0..1integerAverage number of reads representing a given nucleotide in the reconstructed sequence
... repository ∑0..*BackboneElementExternal repository
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
.... url ∑0..1uriURI of the repository
.... name ∑0..1stringName of the repository
.... variantId ∑0..1stringId of the variant
.... readId ∑0..1stringId of the read
... pointer ∑0..*Reference(Sequence)Pointer to next atomic sequence
... observedSeq ∑0..1stringObserved Sequence
... observation ∑0..1Reference(Observation)Observation-genetics
... structureVariation ∑0..1BackboneElement
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
.... precisionOfBoundaries ∑0..1stringPrecision of boundaries
.... reportedaCGHRatio ∑0..1decimalStructural Variant reported aCGH ratio
.... length ∑0..1integerStructural Variant Length
.... outer ∑0..1BackboneElement
..... extension 0..*ExtensionAdditional Content defined by implementations
..... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
..... start ∑0..1integerStructural Variant Outer Start-End
..... end ∑0..1integerStructural Variant Outer Start-End
.... inner ∑0..1BackboneElement
..... extension 0..*ExtensionAdditional Content defined by implementations
..... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
..... start ∑0..1integerStructural Variant Inner Start-End
..... end ∑0..1integerStructural Variant Inner Start-End

doco Documentation for this format

todo

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Sequence ∑0..*SequenceA Sequence
... meta ∑0..1MetaMetadata about the resource
... implicitRules ?! ∑0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: IETF BCP-47 (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... sequence-consensus-sequence-blockPhaseSet 0..1integerPhase Set
URL: http://hl7.org/fhir/StructureDefinition/sequence-consensus-sequence-blockPhaseSet
... sequence-consensus-sequence-blockExpectedCopyNumber 0..1integerExpected Copy Number
URL: http://hl7.org/fhir/StructureDefinition/sequence-consensus-sequence-blockExpectedCopyNumber
... sequence-consensus-sequence-blockContinuity 0..1booleanContinuity
URL: http://hl7.org/fhir/StructureDefinition/sequence-consensus-sequence-blockContinuity
... sequence-consensus-sequence-blockStrand 0..1integerStrand
URL: http://hl7.org/fhir/StructureDefinition/sequence-consensus-sequence-blockStrand
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... type ∑1..1codeAA | DNA | RNA
Binding: sequenceType (example)
... patient ∑0..1Reference(Patient)Who and/or what this is about
... specimen ∑0..1Reference(Specimen)Specimen used for sequencing
... device ∑0..1Reference(Device)The method for sequencing
... quantity ∑0..1QuantityQuantity of the sequence
... species ∑0..1CodeableConceptSupporting tests of human, viruses, and bacteria
Binding: SNOMED CT Codes for species (example)
... referenceSeq ∑0..*BackboneElementReference sequence
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
.... chromosome ∑0..1CodeableConceptThe chromosome containing the genetic finding
Binding: chromosome-human (example)
.... genomeBuild ∑0..1stringThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
.... referenceSeqId ∑1..1CodeableConceptReference identifier
Binding: ENSEMBL (example)
.... referenceSeqPointer ∑0..1Reference(Sequence)A Pointer to another Sequence entity as refence sequence
.... referenceSeqString ∑0..1stringA Reference Sequence string
.... windowStart ∑1..1integer0-based start position (inclusive) of the window on the reference sequence
.... windowEnd ∑1..1integer0-based end position (exclusive) of the window on the reference sequence
... variation ∑0..1BackboneElementVariation info in this sequence
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
.... start ∑0..1integer0-based start position (inclusive) of the variation on the reference sequence
.... end ∑0..1integer0-based end position (exclusive) of the variation on the reference sequence
.... observedAllele ∑0..1stringNucleotide(s)/amino acids from start position to stop position of observed variation
.... referenceAllele ∑0..1stringNucleotide(s)/amino acids from start position to stop position of reference variation
.... cigar ∑0..1stringExtended CIGAR string for aligning the sequence with reference bases
... quality ∑0..*BackboneElementSequence Quality
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
.... start ∑0..1integer0-based start position (inclusive) of the sequence
.... end ∑0..1integer0-based end position (exclusive) of the sequence
.... score ∑0..1QuantityQuality score
.... method ∑0..1stringMethod for quality
... allelicState ∑0..1CodeableConceptThe level of occurrence of a single DNA Sequence Variation within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
Binding: LOINC 53034-5 answerlist (example)
... allelicFrequency ∑0..1decimalAllele frequencies
... copyNumberEvent ∑0..1CodeableConceptCopy Number Event: Values: amplificaiton / deletion / LOH
Binding: CopyNumberEvent (example)
... readCoverage ∑0..1integerAverage number of reads representing a given nucleotide in the reconstructed sequence
... repository ∑0..*BackboneElementExternal repository
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
.... url ∑0..1uriURI of the repository
.... name ∑0..1stringName of the repository
.... variantId ∑0..1stringId of the variant
.... readId ∑0..1stringId of the read
... pointer ∑0..*Reference(Sequence)Pointer to next atomic sequence
... observedSeq ∑0..1stringObserved Sequence
... observation ∑0..1Reference(Observation)Observation-genetics
... structureVariation ∑0..1BackboneElement
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
.... precisionOfBoundaries ∑0..1stringPrecision of boundaries
.... reportedaCGHRatio ∑0..1decimalStructural Variant reported aCGH ratio
.... length ∑0..1integerStructural Variant Length
.... outer ∑0..1BackboneElement
..... extension 0..*ExtensionAdditional Content defined by implementations
..... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
..... start ∑0..1integerStructural Variant Outer Start-End
..... end ∑0..1integerStructural Variant Outer Start-End
.... inner ∑0..1BackboneElement
..... extension 0..*ExtensionAdditional Content defined by implementations
..... modifierExtension ?! ∑0..*ExtensionExtensions that cannot be ignored
..... start ∑0..1integerStructural Variant Inner Start-End
..... end ∑0..1integerStructural Variant Inner Start-End

doco Documentation for this format

XML Template

JSON Template

todo

 

Other representations of profile: Schematron

4.37.10.2.2 Terminology Bindings

PathNameConformanceValueSet
Sequence.language?extrequiredhttp://tools.ietf.org/html/bcp47
Sequence.typesequenceTypeexamplesequenceType
Sequence.speciesSNOMED CT Codes for speciesexampleSNOMED CT Codes for species
Sequence.referenceSeq.chromosomechromosome-humanexamplechromosome-human
Sequence.referenceSeq.referenceSeqIdENSEMBLexampleENSEMBL
Sequence.allelicStateLOINC 53034-5 answerlistexampleLOINC 53034-5 answerlist
Sequence.copyNumberEventCopyNumberEventexampleCopyNumberEvent

4.37.10.2.3 Constraints

IdPathDetailsRequirements
.