Extensions for Using Data Elements from FHIR R4 in FHIR R4B - Downloaded Version null See the Directory of published versions

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Resource Profile: Profile_R4_MolecularSequence_R4B

This cross-version profile allows R4 MolecularSequence content to be represented via FHIR R4B MolecularSequence resources.

Usages:

• This Profile is not used by any profiles in this Implementation Guide

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

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

• Key Elements Table
• Differential Table
• Snapshot Table
• Statistics/References
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Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
MolecularSequence	C	0..*	MolecularSequence(4.3.0)	Information about a biological sequence Constraints: msq-3
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored Constraints: ext-1
coordinateSystem	Σ	1..1	integer	Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
Documentation for this format

Constraints

Id	Grade	Path(s)	Description	Expression
dom-2	error	MolecularSequence	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	MolecularSequence	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource	contained.where(((id.exists() and ('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url)))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(uri) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	MolecularSequence	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	MolecularSequence	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	MolecularSequence	A resource should have narrative for robust management	text.`div`.exists()
ele-1	error	MolecularSequence.implicitRules, MolecularSequence.modifierExtension, MolecularSequence.coordinateSystem	All FHIR elements must have a @value or children	hasValue() or (children().count() > id.count())
ext-1	error	MolecularSequence.modifierExtension	Must have either extensions or value[x], not both	extension.exists() != value.exists()
msq-3	error	MolecularSequence	Only 0 and 1 are valid for coordinateSystem	coordinateSystem = 1 or coordinateSystem = 0

This structure is derived from MolecularSequence

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
MolecularSequence		0..*	MolecularSequence(4.3.0)	Information about a biological sequence
Documentation for this format

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
MolecularSequence	C	0..*	MolecularSequence(4.3.0)	Information about a biological sequence Constraints: msq-3
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): IETF language tag Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements
contained		0..*	Resource	Contained, inline Resources Constraints: dom-r4b
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored Constraints: ext-1
identifier	Σ	0..*	Identifier	Unique ID for this particular sequence. This is a FHIR-defined id
type	Σ	0..1	code	aa | dna | rna Binding: sequenceType (required): Type if a sequence -- DNA, RNA, or amino acid sequence.
coordinateSystem	Σ	1..1	integer	Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
patient	Σ	0..1	Reference(Patient)	Who and/or what this is about
specimen	Σ	0..1	Reference(Specimen)	Specimen used for sequencing
device	Σ	0..1	Reference(Device)	The method for sequencing
performer	Σ	0..1	Reference(Organization)	Who should be responsible for test result
quantity	Σ	0..1	Quantity	The number of copies of the sequence of interest. (RNASeq)
referenceSeq	ΣC	0..1	BackboneElement	A sequence used as reference Constraints: msq-5, msq-6
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
chromosome	Σ	0..1	CodeableConcept	Chromosome containing genetic finding Binding: chromosome-human (example): The chromosome containing the genetic finding
genomeBuild	Σ	0..1	string	The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
orientation	Σ	0..1	code	sense | antisense Binding: orientationType (required): Type for orientation
referenceSeqId	Σ	0..1	CodeableConcept	Reference identifier Binding: ENSEMBL (example): Reference identifier for reference sequence
referenceSeqPointer	Σ	0..1	Reference(MolecularSequence)	A pointer to another MolecularSequence entity as reference sequence
referenceSeqString	Σ	0..1	string	A string to represent reference sequence
strand	Σ	0..1	code	watson | crick Binding: strandType (required): Type for strand
windowStart	Σ	0..1	integer	Start position of the window on the reference sequence
windowEnd	Σ	0..1	integer	End position of the window on the reference sequence
variant	Σ	0..*	BackboneElement	Variant in sequence
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
start	Σ	0..1	integer	Start position of the variant on the reference sequence
end	Σ	0..1	integer	End position of the variant on the reference sequence
observedAllele	Σ	0..1	string	Allele that was observed
referenceAllele	Σ	0..1	string	Allele in the reference sequence
cigar	Σ	0..1	string	Extended CIGAR string for aligning the sequence with reference bases
variantPointer	Σ	0..1	Reference(Observation)	Pointer to observed variant information
observedSeq	Σ	0..1	string	Sequence that was observed
quality	Σ	0..*	BackboneElement	An set of value as quality of sequence
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
type	Σ	1..1	code	indel | snp | unknown Binding: qualityType (required): Type for quality
standardSequence	Σ	0..1	CodeableConcept	Standard sequence for comparison Binding: FDA-StandardSequence (example): Reference identifier for standard sequence
start	Σ	0..1	integer	Start position of the sequence
end	Σ	0..1	integer	End position of the sequence
score	Σ	0..1	Quantity	Quality score for the comparison
method	Σ	0..1	CodeableConcept	Method to get quality Binding: FDA-Method (example): How to get the numerical score
truthTP	Σ	0..1	decimal	True positives from the perspective of the truth data
queryTP	Σ	0..1	decimal	True positives from the perspective of the query data
truthFN	Σ	0..1	decimal	False negatives
queryFP	Σ	0..1	decimal	False positives
gtFP	Σ	0..1	decimal	False positives where the non-REF alleles in the Truth and Query Call Sets match
precision	Σ	0..1	decimal	Precision of comparison
recall	Σ	0..1	decimal	Recall of comparison
fScore	Σ	0..1	decimal	F-score
roc	Σ	0..1	BackboneElement	Receiver Operator Characteristic (ROC) Curve
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
score	Σ	0..*	integer	Genotype quality score
numTP	Σ	0..*	integer	Roc score true positive numbers
numFP	Σ	0..*	integer	Roc score false positive numbers
numFN	Σ	0..*	integer	Roc score false negative numbers
precision	Σ	0..*	decimal	Precision of the GQ score
sensitivity	Σ	0..*	decimal	Sensitivity of the GQ score
fMeasure	Σ	0..*	decimal	FScore of the GQ score
readCoverage	Σ	0..1	integer	Average number of reads representing a given nucleotide in the reconstructed sequence
repository	Σ	0..*	BackboneElement	External repository which contains detailed report related with observedSeq in this resource
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
type	Σ	1..1	code	directlink | openapi | login | oauth | other Binding: repositoryType (required): Type for repository
url	Σ	0..1	uri	URI of the repository
name	Σ	0..1	string	Repository's name
datasetId	Σ	0..1	string	Id of the dataset that used to call for dataset in repository
variantsetId	Σ	0..1	string	Id of the variantset that used to call for variantset in repository
readsetId	Σ	0..1	string	Id of the read
pointer	Σ	0..*	Reference(MolecularSequence)	Pointer to next atomic sequence
structureVariant	Σ	0..*	BackboneElement	Structural variant
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
variantType	Σ	0..1	CodeableConcept	Structural variant change type Binding: LOINC Answer List LL379-9|4.3.0 (required): DNA change type.
exact	Σ	0..1	boolean	Does the structural variant have base pair resolution breakpoints?
length	Σ	0..1	integer	Structural variant length
outer	Σ	0..1	BackboneElement	Structural variant outer
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
start	Σ	0..1	integer	Structural variant outer start
end	Σ	0..1	integer	Structural variant outer end
inner	Σ	0..1	BackboneElement	Structural variant inner
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
start	Σ	0..1	integer	Structural variant inner start
end	Σ	0..1	integer	Structural variant inner end
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
MolecularSequence.language	Base	preferred	Common Languages	📍4.3.0	FHIR Std.
MolecularSequence.type	Base	required	sequenceType	📍4.3.0	FHIR Std.
MolecularSequence.referenceSeq.​chromosome	Base	example	chromosome-human	📍4.3.0	FHIR Std.
MolecularSequence.referenceSeq.​orientation	Base	required	orientationType	📍4.3.0	FHIR Std.
MolecularSequence.referenceSeq.​referenceSeqId	Base	example	ENSEMBL	📍4.3.0	FHIR Std.
MolecularSequence.referenceSeq.​strand	Base	required	strandType	📍4.3.0	FHIR Std.
MolecularSequence.quality.​type	Base	required	qualityType	📍4.3.0	FHIR Std.
MolecularSequence.quality.​standardSequence	Base	example	FDA-StandardSequence	📍4.3.0	FHIR Std.
MolecularSequence.quality.​method	Base	example	FDA-Method	📍4.3.0	FHIR Std.
MolecularSequence.repository.​type	Base	required	repositoryType	📍4.3.0	FHIR Std.
MolecularSequence.structureVariant.​variantType	Base	required	LOINC Answer Codes for LL379-9|4.3.0	📍4.3.0	unknown?

Constraints

Id	Grade	Path(s)	Description	Expression
dom-2	error	MolecularSequence	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	MolecularSequence	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource	contained.where(((id.exists() and ('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url)))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(uri) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	MolecularSequence	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	MolecularSequence	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	MolecularSequence	A resource should have narrative for robust management	text.`div`.exists()
dom-r4b	warning	MolecularSequence.contained	Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems	($this is Citation or $this is Evidence or $this is EvidenceReport or $this is EvidenceVariable or $this is MedicinalProductDefinition or $this is PackagedProductDefinition or $this is AdministrableProductDefinition or $this is Ingredient or $this is ClinicalUseDefinition or $this is RegulatedAuthorization or $this is SubstanceDefinition or $this is SubscriptionStatus or $this is SubscriptionTopic) implies (%resource is Citation or %resource is Evidence or %resource is EvidenceReport or %resource is EvidenceVariable or %resource is MedicinalProductDefinition or %resource is PackagedProductDefinition or %resource is AdministrableProductDefinition or %resource is Ingredient or %resource is ClinicalUseDefinition or %resource is RegulatedAuthorization or %resource is SubstanceDefinition or %resource is SubscriptionStatus or %resource is SubscriptionTopic)
ele-1	error	MolecularSequence.meta, MolecularSequence.implicitRules, MolecularSequence.language, MolecularSequence.text, MolecularSequence.extension, MolecularSequence.modifierExtension, MolecularSequence.identifier, MolecularSequence.type, MolecularSequence.coordinateSystem, MolecularSequence.patient, MolecularSequence.specimen, MolecularSequence.device, MolecularSequence.performer, MolecularSequence.quantity, MolecularSequence.referenceSeq, MolecularSequence.referenceSeq.extension, MolecularSequence.referenceSeq.modifierExtension, MolecularSequence.referenceSeq.chromosome, MolecularSequence.referenceSeq.genomeBuild, MolecularSequence.referenceSeq.orientation, MolecularSequence.referenceSeq.referenceSeqId, MolecularSequence.referenceSeq.referenceSeqPointer, MolecularSequence.referenceSeq.referenceSeqString, MolecularSequence.referenceSeq.strand, MolecularSequence.referenceSeq.windowStart, MolecularSequence.referenceSeq.windowEnd, MolecularSequence.variant, MolecularSequence.variant.extension, MolecularSequence.variant.modifierExtension, MolecularSequence.variant.start, MolecularSequence.variant.end, MolecularSequence.variant.observedAllele, MolecularSequence.variant.referenceAllele, MolecularSequence.variant.cigar, MolecularSequence.variant.variantPointer, MolecularSequence.observedSeq, MolecularSequence.quality, MolecularSequence.quality.extension, MolecularSequence.quality.modifierExtension, MolecularSequence.quality.type, MolecularSequence.quality.standardSequence, MolecularSequence.quality.start, MolecularSequence.quality.end, MolecularSequence.quality.score, MolecularSequence.quality.method, MolecularSequence.quality.truthTP, MolecularSequence.quality.queryTP, MolecularSequence.quality.truthFN, MolecularSequence.quality.queryFP, MolecularSequence.quality.gtFP, MolecularSequence.quality.precision, MolecularSequence.quality.recall, MolecularSequence.quality.fScore, MolecularSequence.quality.roc, MolecularSequence.quality.roc.extension, MolecularSequence.quality.roc.modifierExtension, MolecularSequence.quality.roc.score, MolecularSequence.quality.roc.numTP, MolecularSequence.quality.roc.numFP, MolecularSequence.quality.roc.numFN, MolecularSequence.quality.roc.precision, MolecularSequence.quality.roc.sensitivity, MolecularSequence.quality.roc.fMeasure, MolecularSequence.readCoverage, MolecularSequence.repository, MolecularSequence.repository.extension, MolecularSequence.repository.modifierExtension, MolecularSequence.repository.type, MolecularSequence.repository.url, MolecularSequence.repository.name, MolecularSequence.repository.datasetId, MolecularSequence.repository.variantsetId, MolecularSequence.repository.readsetId, MolecularSequence.pointer, MolecularSequence.structureVariant, MolecularSequence.structureVariant.extension, MolecularSequence.structureVariant.modifierExtension, MolecularSequence.structureVariant.variantType, MolecularSequence.structureVariant.exact, MolecularSequence.structureVariant.length, MolecularSequence.structureVariant.outer, MolecularSequence.structureVariant.outer.extension, MolecularSequence.structureVariant.outer.modifierExtension, MolecularSequence.structureVariant.outer.start, MolecularSequence.structureVariant.outer.end, MolecularSequence.structureVariant.inner, MolecularSequence.structureVariant.inner.extension, MolecularSequence.structureVariant.inner.modifierExtension, MolecularSequence.structureVariant.inner.start, MolecularSequence.structureVariant.inner.end	All FHIR elements must have a @value or children	hasValue() or (children().count() > id.count())
ext-1	error	MolecularSequence.extension, MolecularSequence.modifierExtension, MolecularSequence.referenceSeq.extension, MolecularSequence.referenceSeq.modifierExtension, MolecularSequence.variant.extension, MolecularSequence.variant.modifierExtension, MolecularSequence.quality.extension, MolecularSequence.quality.modifierExtension, MolecularSequence.quality.roc.extension, MolecularSequence.quality.roc.modifierExtension, MolecularSequence.repository.extension, MolecularSequence.repository.modifierExtension, MolecularSequence.structureVariant.extension, MolecularSequence.structureVariant.modifierExtension, MolecularSequence.structureVariant.outer.extension, MolecularSequence.structureVariant.outer.modifierExtension, MolecularSequence.structureVariant.inner.extension, MolecularSequence.structureVariant.inner.modifierExtension	Must have either extensions or value[x], not both	extension.exists() != value.exists()
msq-3	error	MolecularSequence	Only 0 and 1 are valid for coordinateSystem	coordinateSystem = 1 or coordinateSystem = 0
msq-5	error	MolecularSequence.referenceSeq	GenomeBuild and chromosome must be both contained if either one of them is contained	(chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())
msq-6	error	MolecularSequence.referenceSeq	Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;	(genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1

This structure is derived from MolecularSequence

Summary

Maturity: 0

Key Elements View

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
MolecularSequence	C	0..*	MolecularSequence(4.3.0)	Information about a biological sequence Constraints: msq-3
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored Constraints: ext-1
coordinateSystem	Σ	1..1	integer	Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
Documentation for this format

Constraints

Id	Grade	Path(s)	Description	Expression
dom-2	error	MolecularSequence	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	MolecularSequence	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource	contained.where(((id.exists() and ('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url)))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(uri) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	MolecularSequence	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	MolecularSequence	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	MolecularSequence	A resource should have narrative for robust management	text.`div`.exists()
ele-1	error	MolecularSequence.implicitRules, MolecularSequence.modifierExtension, MolecularSequence.coordinateSystem	All FHIR elements must have a @value or children	hasValue() or (children().count() > id.count())
ext-1	error	MolecularSequence.modifierExtension	Must have either extensions or value[x], not both	extension.exists() != value.exists()
msq-3	error	MolecularSequence	Only 0 and 1 are valid for coordinateSystem	coordinateSystem = 1 or coordinateSystem = 0

Differential View

This structure is derived from MolecularSequence

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
MolecularSequence		0..*	MolecularSequence(4.3.0)	Information about a biological sequence
Documentation for this format

Snapshot View

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
MolecularSequence	C	0..*	MolecularSequence(4.3.0)	Information about a biological sequence Constraints: msq-3
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): IETF language tag Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements
contained		0..*	Resource	Contained, inline Resources Constraints: dom-r4b
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored Constraints: ext-1
identifier	Σ	0..*	Identifier	Unique ID for this particular sequence. This is a FHIR-defined id
type	Σ	0..1	code	aa | dna | rna Binding: sequenceType (required): Type if a sequence -- DNA, RNA, or amino acid sequence.
coordinateSystem	Σ	1..1	integer	Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
patient	Σ	0..1	Reference(Patient)	Who and/or what this is about
specimen	Σ	0..1	Reference(Specimen)	Specimen used for sequencing
device	Σ	0..1	Reference(Device)	The method for sequencing
performer	Σ	0..1	Reference(Organization)	Who should be responsible for test result
quantity	Σ	0..1	Quantity	The number of copies of the sequence of interest. (RNASeq)
referenceSeq	ΣC	0..1	BackboneElement	A sequence used as reference Constraints: msq-5, msq-6
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
chromosome	Σ	0..1	CodeableConcept	Chromosome containing genetic finding Binding: chromosome-human (example): The chromosome containing the genetic finding
genomeBuild	Σ	0..1	string	The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
orientation	Σ	0..1	code	sense | antisense Binding: orientationType (required): Type for orientation
referenceSeqId	Σ	0..1	CodeableConcept	Reference identifier Binding: ENSEMBL (example): Reference identifier for reference sequence
referenceSeqPointer	Σ	0..1	Reference(MolecularSequence)	A pointer to another MolecularSequence entity as reference sequence
referenceSeqString	Σ	0..1	string	A string to represent reference sequence
strand	Σ	0..1	code	watson | crick Binding: strandType (required): Type for strand
windowStart	Σ	0..1	integer	Start position of the window on the reference sequence
windowEnd	Σ	0..1	integer	End position of the window on the reference sequence
variant	Σ	0..*	BackboneElement	Variant in sequence
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
start	Σ	0..1	integer	Start position of the variant on the reference sequence
end	Σ	0..1	integer	End position of the variant on the reference sequence
observedAllele	Σ	0..1	string	Allele that was observed
referenceAllele	Σ	0..1	string	Allele in the reference sequence
cigar	Σ	0..1	string	Extended CIGAR string for aligning the sequence with reference bases
variantPointer	Σ	0..1	Reference(Observation)	Pointer to observed variant information
observedSeq	Σ	0..1	string	Sequence that was observed
quality	Σ	0..*	BackboneElement	An set of value as quality of sequence
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
type	Σ	1..1	code	indel | snp | unknown Binding: qualityType (required): Type for quality
standardSequence	Σ	0..1	CodeableConcept	Standard sequence for comparison Binding: FDA-StandardSequence (example): Reference identifier for standard sequence
start	Σ	0..1	integer	Start position of the sequence
end	Σ	0..1	integer	End position of the sequence
score	Σ	0..1	Quantity	Quality score for the comparison
method	Σ	0..1	CodeableConcept	Method to get quality Binding: FDA-Method (example): How to get the numerical score
truthTP	Σ	0..1	decimal	True positives from the perspective of the truth data
queryTP	Σ	0..1	decimal	True positives from the perspective of the query data
truthFN	Σ	0..1	decimal	False negatives
queryFP	Σ	0..1	decimal	False positives
gtFP	Σ	0..1	decimal	False positives where the non-REF alleles in the Truth and Query Call Sets match
precision	Σ	0..1	decimal	Precision of comparison
recall	Σ	0..1	decimal	Recall of comparison
fScore	Σ	0..1	decimal	F-score
roc	Σ	0..1	BackboneElement	Receiver Operator Characteristic (ROC) Curve
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
score	Σ	0..*	integer	Genotype quality score
numTP	Σ	0..*	integer	Roc score true positive numbers
numFP	Σ	0..*	integer	Roc score false positive numbers
numFN	Σ	0..*	integer	Roc score false negative numbers
precision	Σ	0..*	decimal	Precision of the GQ score
sensitivity	Σ	0..*	decimal	Sensitivity of the GQ score
fMeasure	Σ	0..*	decimal	FScore of the GQ score
readCoverage	Σ	0..1	integer	Average number of reads representing a given nucleotide in the reconstructed sequence
repository	Σ	0..*	BackboneElement	External repository which contains detailed report related with observedSeq in this resource
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
type	Σ	1..1	code	directlink | openapi | login | oauth | other Binding: repositoryType (required): Type for repository
url	Σ	0..1	uri	URI of the repository
name	Σ	0..1	string	Repository's name
datasetId	Σ	0..1	string	Id of the dataset that used to call for dataset in repository
variantsetId	Σ	0..1	string	Id of the variantset that used to call for variantset in repository
readsetId	Σ	0..1	string	Id of the read
pointer	Σ	0..*	Reference(MolecularSequence)	Pointer to next atomic sequence
structureVariant	Σ	0..*	BackboneElement	Structural variant
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
variantType	Σ	0..1	CodeableConcept	Structural variant change type Binding: LOINC Answer List LL379-9|4.3.0 (required): DNA change type.
exact	Σ	0..1	boolean	Does the structural variant have base pair resolution breakpoints?
length	Σ	0..1	integer	Structural variant length
outer	Σ	0..1	BackboneElement	Structural variant outer
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
start	Σ	0..1	integer	Structural variant outer start
end	Σ	0..1	integer	Structural variant outer end
inner	Σ	0..1	BackboneElement	Structural variant inner
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Constraints: ext-1
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized Constraints: ext-1
start	Σ	0..1	integer	Structural variant inner start
end	Σ	0..1	integer	Structural variant inner end
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
MolecularSequence.language	Base	preferred	Common Languages	📍4.3.0	FHIR Std.
MolecularSequence.type	Base	required	sequenceType	📍4.3.0	FHIR Std.
MolecularSequence.referenceSeq.​chromosome	Base	example	chromosome-human	📍4.3.0	FHIR Std.
MolecularSequence.referenceSeq.​orientation	Base	required	orientationType	📍4.3.0	FHIR Std.
MolecularSequence.referenceSeq.​referenceSeqId	Base	example	ENSEMBL	📍4.3.0	FHIR Std.
MolecularSequence.referenceSeq.​strand	Base	required	strandType	📍4.3.0	FHIR Std.
MolecularSequence.quality.​type	Base	required	qualityType	📍4.3.0	FHIR Std.
MolecularSequence.quality.​standardSequence	Base	example	FDA-StandardSequence	📍4.3.0	FHIR Std.
MolecularSequence.quality.​method	Base	example	FDA-Method	📍4.3.0	FHIR Std.
MolecularSequence.repository.​type	Base	required	repositoryType	📍4.3.0	FHIR Std.
MolecularSequence.structureVariant.​variantType	Base	required	LOINC Answer Codes for LL379-9|4.3.0	📍4.3.0	unknown?

Constraints

Id	Grade	Path(s)	Description	Expression
dom-2	error	MolecularSequence	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	MolecularSequence	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource	contained.where(((id.exists() and ('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url)))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(uri) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	MolecularSequence	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	MolecularSequence	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	MolecularSequence	A resource should have narrative for robust management	text.`div`.exists()
dom-r4b	warning	MolecularSequence.contained	Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems	($this is Citation or $this is Evidence or $this is EvidenceReport or $this is EvidenceVariable or $this is MedicinalProductDefinition or $this is PackagedProductDefinition or $this is AdministrableProductDefinition or $this is Ingredient or $this is ClinicalUseDefinition or $this is RegulatedAuthorization or $this is SubstanceDefinition or $this is SubscriptionStatus or $this is SubscriptionTopic) implies (%resource is Citation or %resource is Evidence or %resource is EvidenceReport or %resource is EvidenceVariable or %resource is MedicinalProductDefinition or %resource is PackagedProductDefinition or %resource is AdministrableProductDefinition or %resource is Ingredient or %resource is ClinicalUseDefinition or %resource is RegulatedAuthorization or %resource is SubstanceDefinition or %resource is SubscriptionStatus or %resource is SubscriptionTopic)
ele-1	error	MolecularSequence.meta, MolecularSequence.implicitRules, MolecularSequence.language, MolecularSequence.text, MolecularSequence.extension, MolecularSequence.modifierExtension, MolecularSequence.identifier, MolecularSequence.type, MolecularSequence.coordinateSystem, MolecularSequence.patient, MolecularSequence.specimen, MolecularSequence.device, MolecularSequence.performer, MolecularSequence.quantity, MolecularSequence.referenceSeq, MolecularSequence.referenceSeq.extension, MolecularSequence.referenceSeq.modifierExtension, MolecularSequence.referenceSeq.chromosome, MolecularSequence.referenceSeq.genomeBuild, MolecularSequence.referenceSeq.orientation, MolecularSequence.referenceSeq.referenceSeqId, MolecularSequence.referenceSeq.referenceSeqPointer, MolecularSequence.referenceSeq.referenceSeqString, MolecularSequence.referenceSeq.strand, MolecularSequence.referenceSeq.windowStart, MolecularSequence.referenceSeq.windowEnd, MolecularSequence.variant, MolecularSequence.variant.extension, MolecularSequence.variant.modifierExtension, MolecularSequence.variant.start, MolecularSequence.variant.end, MolecularSequence.variant.observedAllele, MolecularSequence.variant.referenceAllele, MolecularSequence.variant.cigar, MolecularSequence.variant.variantPointer, MolecularSequence.observedSeq, MolecularSequence.quality, MolecularSequence.quality.extension, MolecularSequence.quality.modifierExtension, MolecularSequence.quality.type, MolecularSequence.quality.standardSequence, MolecularSequence.quality.start, MolecularSequence.quality.end, MolecularSequence.quality.score, MolecularSequence.quality.method, MolecularSequence.quality.truthTP, MolecularSequence.quality.queryTP, MolecularSequence.quality.truthFN, MolecularSequence.quality.queryFP, MolecularSequence.quality.gtFP, MolecularSequence.quality.precision, MolecularSequence.quality.recall, MolecularSequence.quality.fScore, MolecularSequence.quality.roc, MolecularSequence.quality.roc.extension, MolecularSequence.quality.roc.modifierExtension, MolecularSequence.quality.roc.score, MolecularSequence.quality.roc.numTP, MolecularSequence.quality.roc.numFP, MolecularSequence.quality.roc.numFN, MolecularSequence.quality.roc.precision, MolecularSequence.quality.roc.sensitivity, MolecularSequence.quality.roc.fMeasure, MolecularSequence.readCoverage, MolecularSequence.repository, MolecularSequence.repository.extension, MolecularSequence.repository.modifierExtension, MolecularSequence.repository.type, MolecularSequence.repository.url, MolecularSequence.repository.name, MolecularSequence.repository.datasetId, MolecularSequence.repository.variantsetId, MolecularSequence.repository.readsetId, MolecularSequence.pointer, MolecularSequence.structureVariant, MolecularSequence.structureVariant.extension, MolecularSequence.structureVariant.modifierExtension, MolecularSequence.structureVariant.variantType, MolecularSequence.structureVariant.exact, MolecularSequence.structureVariant.length, MolecularSequence.structureVariant.outer, MolecularSequence.structureVariant.outer.extension, MolecularSequence.structureVariant.outer.modifierExtension, MolecularSequence.structureVariant.outer.start, MolecularSequence.structureVariant.outer.end, MolecularSequence.structureVariant.inner, MolecularSequence.structureVariant.inner.extension, MolecularSequence.structureVariant.inner.modifierExtension, MolecularSequence.structureVariant.inner.start, MolecularSequence.structureVariant.inner.end	All FHIR elements must have a @value or children	hasValue() or (children().count() > id.count())
ext-1	error	MolecularSequence.extension, MolecularSequence.modifierExtension, MolecularSequence.referenceSeq.extension, MolecularSequence.referenceSeq.modifierExtension, MolecularSequence.variant.extension, MolecularSequence.variant.modifierExtension, MolecularSequence.quality.extension, MolecularSequence.quality.modifierExtension, MolecularSequence.quality.roc.extension, MolecularSequence.quality.roc.modifierExtension, MolecularSequence.repository.extension, MolecularSequence.repository.modifierExtension, MolecularSequence.structureVariant.extension, MolecularSequence.structureVariant.modifierExtension, MolecularSequence.structureVariant.outer.extension, MolecularSequence.structureVariant.outer.modifierExtension, MolecularSequence.structureVariant.inner.extension, MolecularSequence.structureVariant.inner.modifierExtension	Must have either extensions or value[x], not both	extension.exists() != value.exists()
msq-3	error	MolecularSequence	Only 0 and 1 are valid for coordinateSystem	coordinateSystem = 1 or coordinateSystem = 0
msq-5	error	MolecularSequence.referenceSeq	GenomeBuild and chromosome must be both contained if either one of them is contained	(chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())
msq-6	error	MolecularSequence.referenceSeq	Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;	(genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1

This structure is derived from MolecularSequence

Summary

Maturity: 0

Other representations of profile: CSV, Excel, Schematron