HLA Reporting Implementation Guide
0.0.1 - Draft

This page is part of the HLA Reporting Implementation Guide (v0.0.1: Trial Use: 1) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions

StructureDefinition: HLAMolecularSequence

HLA profile of MolecularSequence resource

The official URL for this profile is: 

http://fhir.nmdp.org/ig/hla-reporting/StructureDefinition/hla-molecularsequence

Formal Views of Profile Content

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

This structure is derived from MolecularSequence

Summary

Mandatory: 3 elements
Must-Support: 2 elements

This structure is derived from MolecularSequence

NameFlagsCard.TypeDescription & Constraintsdoco
.. MolecularSequence 0..*MolecularSequenceInformation about a biological sequence
... type 0..1codeaa | dna | rna
Required Pattern: dna
... coordinateSystem 1..1integerBase number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
Required Pattern: 0
... referenceSeq S1..1BackboneElementA sequence used as reference
.... referenceSeqId 1..1CodeableConceptReference identifier
Required Pattern: At least the following
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... system1..1uriIdentity of the terminology system
Fixed Value: http://www.ebi.ac.uk/ipd/imgt/hla

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. MolecularSequence I0..*MolecularSequenceInformation about a biological sequence
... id Σ0..1stringLogical id of this artifact
... meta ΣI0..1MetaMetadata about the resource
... implicitRules ?!ΣI0..1uriA set of rules under which this content was created
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension I0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!I0..*ExtensionExtensions that cannot be ignored
... identifier ΣI0..*IdentifierUnique ID for this particular sequence. This is a FHIR-defined id
... type ΣI0..1codeaa | dna | rna
Binding: sequenceType (required)
Required Pattern: dna
... coordinateSystem ΣI1..1integerBase number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
Required Pattern: 0
... patient ΣI0..1Reference(Patient)Who and/or what this is about
... specimen ΣI0..1Reference(Specimen)Specimen used for sequencing
... device ΣI0..1Reference(Device)The method for sequencing
... performer ΣI0..1Reference(Organization)Who should be responsible for test result
... quantity ΣI0..1QuantityThe number of copies of the sequence of interest. (RNASeq)
... referenceSeq SΣI1..1BackboneElementA sequence used as reference
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... chromosome ΣI0..1CodeableConceptChromosome containing genetic finding
Binding: chromosome-human (example)
.... genomeBuild ΣI0..1stringThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
.... orientation ΣI0..1codesense | antisense
Binding: orientationType (required)
.... referenceSeqId ΣI1..1CodeableConceptReference identifier
Binding: ENSEMBL (example)
Required Pattern: At least the following
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://www.ebi.ac.uk/ipd/imgt/hla
...... version0..1stringVersion of the system - if relevant
...... code0..1codeSymbol in syntax defined by the system
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text0..1stringPlain text representation of the concept
.... referenceSeqPointer ΣI0..1Reference(MolecularSequence)A pointer to another MolecularSequence entity as reference sequence
.... referenceSeqString ΣI0..1stringA string to represent reference sequence
.... strand ΣI0..1codewatson | crick
Binding: strandType (required)
.... windowStart ΣI0..1integerStart position of the window on the reference sequence
.... windowEnd ΣI0..1integerEnd position of the window on the reference sequence
... variant ΣI0..*BackboneElementVariant in sequence
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... start ΣI0..1integerStart position of the variant on the reference sequence
.... end ΣI0..1integerEnd position of the variant on the reference sequence
.... observedAllele ΣI0..1stringAllele that was observed
.... referenceAllele ΣI0..1stringAllele in the reference sequence
.... cigar ΣI0..1stringExtended CIGAR string for aligning the sequence with reference bases
.... variantPointer ΣI0..1Reference(Observation)Pointer to observed variant information
... observedSeq SΣI1..1stringSequence that was observed
... quality ΣI0..*BackboneElementAn set of value as quality of sequence
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... type ΣI1..1codeindel | snp | unknown
Binding: qualityType (required)
.... standardSequence ΣI0..1CodeableConceptStandard sequence for comparison
Binding: FDA-StandardSequence (example)
.... start ΣI0..1integerStart position of the sequence
.... end ΣI0..1integerEnd position of the sequence
.... score ΣI0..1QuantityQuality score for the comparison
.... method ΣI0..1CodeableConceptMethod to get quality
Binding: FDA-Method (example)
.... truthTP ΣI0..1decimalTrue positives from the perspective of the truth data
.... queryTP ΣI0..1decimalTrue positives from the perspective of the query data
.... truthFN ΣI0..1decimalFalse negatives
.... queryFP ΣI0..1decimalFalse positives
.... gtFP ΣI0..1decimalFalse positives where the non-REF alleles in the Truth and Query Call Sets match
.... precision ΣI0..1decimalPrecision of comparison
.... recall ΣI0..1decimalRecall of comparison
.... fScore ΣI0..1decimalF-score
.... roc ΣI0..1BackboneElementReceiver Operator Characteristic (ROC) Curve
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... score ΣI0..*integerGenotype quality score
..... numTP ΣI0..*integerRoc score true positive numbers
..... numFP ΣI0..*integerRoc score false positive numbers
..... numFN ΣI0..*integerRoc score false negative numbers
..... precision ΣI0..*decimalPrecision of the GQ score
..... sensitivity ΣI0..*decimalSensitivity of the GQ score
..... fMeasure ΣI0..*decimalFScore of the GQ score
... readCoverage ΣI0..1integerAverage number of reads representing a given nucleotide in the reconstructed sequence
... repository ΣI0..*BackboneElementExternal repository which contains detailed report related with observedSeq in this resource
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... type ΣI1..1codedirectlink | openapi | login | oauth | other
Binding: repositoryType (required)
.... url ΣI0..1uriURI of the repository
.... name ΣI0..1stringRepository's name
.... datasetId ΣI0..1stringId of the dataset that used to call for dataset in repository
.... variantsetId ΣI0..1stringId of the variantset that used to call for variantset in repository
.... readsetId ΣI0..1stringId of the read
... pointer ΣI0..*Reference(MolecularSequence)Pointer to next atomic sequence
... structureVariant ΣI0..*BackboneElementStructural variant
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... variantType ΣI0..1CodeableConceptStructural variant change type
Binding: LOINC Answer List LL379-9|4.0.1 (required)
.... exact ΣI0..1booleanDoes the structural variant have base pair resolution breakpoints?
.... length ΣI0..1integerStructural variant length
.... outer ΣI0..1BackboneElementStructural variant outer
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... start ΣI0..1integerStructural variant outer start
..... end ΣI0..1integerStructural variant outer end
.... inner ΣI0..1BackboneElementStructural variant inner
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... start ΣI0..1integerStructural variant inner start
..... end ΣI0..1integerStructural variant inner end

doco Documentation for this format

This structure is derived from MolecularSequence

Summary

Mandatory: 3 elements
Must-Support: 2 elements

Differential View

This structure is derived from MolecularSequence

NameFlagsCard.TypeDescription & Constraintsdoco
.. MolecularSequence 0..*MolecularSequenceInformation about a biological sequence
... type 0..1codeaa | dna | rna
Required Pattern: dna
... coordinateSystem 1..1integerBase number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
Required Pattern: 0
... referenceSeq S1..1BackboneElementA sequence used as reference
.... referenceSeqId 1..1CodeableConceptReference identifier
Required Pattern: At least the following
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... system1..1uriIdentity of the terminology system
Fixed Value: http://www.ebi.ac.uk/ipd/imgt/hla

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. MolecularSequence I0..*MolecularSequenceInformation about a biological sequence
... id Σ0..1stringLogical id of this artifact
... meta ΣI0..1MetaMetadata about the resource
... implicitRules ?!ΣI0..1uriA set of rules under which this content was created
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension I0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!I0..*ExtensionExtensions that cannot be ignored
... identifier ΣI0..*IdentifierUnique ID for this particular sequence. This is a FHIR-defined id
... type ΣI0..1codeaa | dna | rna
Binding: sequenceType (required)
Required Pattern: dna
... coordinateSystem ΣI1..1integerBase number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
Required Pattern: 0
... patient ΣI0..1Reference(Patient)Who and/or what this is about
... specimen ΣI0..1Reference(Specimen)Specimen used for sequencing
... device ΣI0..1Reference(Device)The method for sequencing
... performer ΣI0..1Reference(Organization)Who should be responsible for test result
... quantity ΣI0..1QuantityThe number of copies of the sequence of interest. (RNASeq)
... referenceSeq SΣI1..1BackboneElementA sequence used as reference
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... chromosome ΣI0..1CodeableConceptChromosome containing genetic finding
Binding: chromosome-human (example)
.... genomeBuild ΣI0..1stringThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
.... orientation ΣI0..1codesense | antisense
Binding: orientationType (required)
.... referenceSeqId ΣI1..1CodeableConceptReference identifier
Binding: ENSEMBL (example)
Required Pattern: At least the following
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://www.ebi.ac.uk/ipd/imgt/hla
...... version0..1stringVersion of the system - if relevant
...... code0..1codeSymbol in syntax defined by the system
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text0..1stringPlain text representation of the concept
.... referenceSeqPointer ΣI0..1Reference(MolecularSequence)A pointer to another MolecularSequence entity as reference sequence
.... referenceSeqString ΣI0..1stringA string to represent reference sequence
.... strand ΣI0..1codewatson | crick
Binding: strandType (required)
.... windowStart ΣI0..1integerStart position of the window on the reference sequence
.... windowEnd ΣI0..1integerEnd position of the window on the reference sequence
... variant ΣI0..*BackboneElementVariant in sequence
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... start ΣI0..1integerStart position of the variant on the reference sequence
.... end ΣI0..1integerEnd position of the variant on the reference sequence
.... observedAllele ΣI0..1stringAllele that was observed
.... referenceAllele ΣI0..1stringAllele in the reference sequence
.... cigar ΣI0..1stringExtended CIGAR string for aligning the sequence with reference bases
.... variantPointer ΣI0..1Reference(Observation)Pointer to observed variant information
... observedSeq SΣI1..1stringSequence that was observed
... quality ΣI0..*BackboneElementAn set of value as quality of sequence
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... type ΣI1..1codeindel | snp | unknown
Binding: qualityType (required)
.... standardSequence ΣI0..1CodeableConceptStandard sequence for comparison
Binding: FDA-StandardSequence (example)
.... start ΣI0..1integerStart position of the sequence
.... end ΣI0..1integerEnd position of the sequence
.... score ΣI0..1QuantityQuality score for the comparison
.... method ΣI0..1CodeableConceptMethod to get quality
Binding: FDA-Method (example)
.... truthTP ΣI0..1decimalTrue positives from the perspective of the truth data
.... queryTP ΣI0..1decimalTrue positives from the perspective of the query data
.... truthFN ΣI0..1decimalFalse negatives
.... queryFP ΣI0..1decimalFalse positives
.... gtFP ΣI0..1decimalFalse positives where the non-REF alleles in the Truth and Query Call Sets match
.... precision ΣI0..1decimalPrecision of comparison
.... recall ΣI0..1decimalRecall of comparison
.... fScore ΣI0..1decimalF-score
.... roc ΣI0..1BackboneElementReceiver Operator Characteristic (ROC) Curve
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... score ΣI0..*integerGenotype quality score
..... numTP ΣI0..*integerRoc score true positive numbers
..... numFP ΣI0..*integerRoc score false positive numbers
..... numFN ΣI0..*integerRoc score false negative numbers
..... precision ΣI0..*decimalPrecision of the GQ score
..... sensitivity ΣI0..*decimalSensitivity of the GQ score
..... fMeasure ΣI0..*decimalFScore of the GQ score
... readCoverage ΣI0..1integerAverage number of reads representing a given nucleotide in the reconstructed sequence
... repository ΣI0..*BackboneElementExternal repository which contains detailed report related with observedSeq in this resource
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... type ΣI1..1codedirectlink | openapi | login | oauth | other
Binding: repositoryType (required)
.... url ΣI0..1uriURI of the repository
.... name ΣI0..1stringRepository's name
.... datasetId ΣI0..1stringId of the dataset that used to call for dataset in repository
.... variantsetId ΣI0..1stringId of the variantset that used to call for variantset in repository
.... readsetId ΣI0..1stringId of the read
... pointer ΣI0..*Reference(MolecularSequence)Pointer to next atomic sequence
... structureVariant ΣI0..*BackboneElementStructural variant
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... variantType ΣI0..1CodeableConceptStructural variant change type
Binding: LOINC Answer List LL379-9|4.0.1 (required)
.... exact ΣI0..1booleanDoes the structural variant have base pair resolution breakpoints?
.... length ΣI0..1integerStructural variant length
.... outer ΣI0..1BackboneElementStructural variant outer
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... start ΣI0..1integerStructural variant outer start
..... end ΣI0..1integerStructural variant outer end
.... inner ΣI0..1BackboneElementStructural variant inner
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... start ΣI0..1integerStructural variant inner start
..... end ΣI0..1integerStructural variant inner end

doco Documentation for this format

 

Other representations of profile: Schematron

Terminology Bindings

Terminology Bindings

PathConformanceValueSet / Code
MolecularSequence.languagepreferredCommonLanguages
Max Binding: AllLanguages
MolecularSequence.typerequiredPattern: dna
MolecularSequence.referenceSeq.chromosomeexamplechromosome-human
MolecularSequence.referenceSeq.orientationrequiredorientationType
MolecularSequence.referenceSeq.referenceSeqIdexamplePattern: null
MolecularSequence.referenceSeq.strandrequiredstrandType
MolecularSequence.quality.typerequiredqualityType
MolecularSequence.quality.standardSequenceexampleFDA-StandardSequence
MolecularSequence.quality.methodexampleFDA-Method
MolecularSequence.repository.typerequiredrepositoryType
MolecularSequence.structureVariant.variantTyperequiredLOINC LL379-9|4.0.1

Constraints

Constraints

IdPathDetailsRequirements