Extensions for Using Data Elements from FHIR R5 in FHIR STU3
0.1.0 - STU International flag

Extensions for Using Data Elements from FHIR R5 in FHIR STU3 - Downloaded Version null See the Directory of published versions

Resource Profile: Profile_R5_MolecularSequence_R3_Sequence

Official URL: http://hl7.org/fhir/5.0/StructureDefinition/profile-MolecularSequence-for-Sequence Version: 0.1.0
Standards status: Trial-use Maturity Level: 0 Computable Name: Profile_R5_MolecularSequence_R3_Sequence

This cross-version profile allows R5 MolecularSequence content to be represented via FHIR STU3 Sequence resources.

Usages:

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.

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Sequence C 0..* Sequence Information about a biological sequence
Constraints: seq-3
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:focus 0..* Reference(Cross-version Profile for R5.Resource for use in FHIR STU3(0.1.0) | Resource) R5: What the molecular sequence is about, when it is not about the subject of record (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.focus
.... extension:formatted 0..* Attachment R5: Embedded file or a link (URL) which contains content to represent the sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.formatted
.... extension:coordinateSystem 1..1 CodeableConcept R5: Ways of identifying nucleotides or amino acids within a sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem
.... extension:ordinalPosition 0..1 integer R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition
.... extension:sequenceRange 0..1 Range R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored

doco Documentation for this format

Constraints

Id Grade Path(s) Description Expression
dom-1 error Sequence If the resource is contained in another resource, it SHALL NOT contain any narrative contained.text.empty()
dom-2 error Sequence If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Sequence If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource contained.where(('#'+id in %resource.descendants().reference).not()).empty()
dom-4 error Sequence 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()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() | (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
seq-3 error Sequence Only 0 and 1 are valid for coordinateSystem coordinateSystem = 1 or coordinateSystem = 0

This structure is derived from Sequence

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Sequence 0..* Sequence Information about a biological sequence
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:focus 0..* Reference(Cross-version Profile for R5.Resource for use in FHIR STU3(0.1.0) | Resource) R5: What the molecular sequence is about, when it is not about the subject of record (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.focus
.... extension:formatted 0..* Attachment R5: Embedded file or a link (URL) which contains content to represent the sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.formatted
.... extension:coordinateSystem 1..1 CodeableConcept R5: Ways of identifying nucleotides or amino acids within a sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem
.... extension:ordinalPosition 0..1 integer R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition
.... extension:sequenceRange 0..1 Range R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange
... type
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:type 0..1 code R5: type
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.type
Binding: sequenceType (required): Type if a sequence -- DNA, RNA, or amino acid sequence.
... patient
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:subject 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: Subject this sequence is associated too
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:specimen 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: specimen additional types
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
... device
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:device 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: device additional types
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
... performer
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:performer 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: performer additional types
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
... referenceSeq
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:genomeAssembly 0..1 CodeableConcept R5: The genome assembly used for starting sequence, e.g. GRCh38 (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.genomeAssembly
..... extension:sequence 0..1 CodeableConcept, Reference(Cross-version Profile for R5.MolecularSequence for use in FHIR STU3(0.1.0) | Sequence) R5: The reference sequence that represents the starting sequence additional types
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence
..... extension:orientation 0..1 code R5: sense | antisense (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.orientation
Binding: R5OrientationTypeForR3 (0.1.0) (required): Type for orientation
.... chromosome
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
...... extension:chromosome 0..1 CodeableConcept R5: Chromosome Identifier
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome
.... strand
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
...... extension:strand 0..1 code R5: watson | crick additional types
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.strand
Binding: R5StrandTypeForR3 (0.1.0) (required): Type for strand
... variant
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:start 0..1 integer R5: Start position of the edit on the starting sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.edit.start

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Sequence C 0..* Sequence Information about a biological sequence
Constraints: seq-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
... 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
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:focus 0..* Reference(Cross-version Profile for R5.Resource for use in FHIR STU3(0.1.0) | Resource) R5: What the molecular sequence is about, when it is not about the subject of record (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.focus
.... extension:formatted 0..* Attachment R5: Embedded file or a link (URL) which contains content to represent the sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.formatted
.... extension:coordinateSystem 1..1 CodeableConcept R5: Ways of identifying nucleotides or amino acids within a sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem
.... extension:ordinalPosition 0..1 integer R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition
.... extension:sequenceRange 0..1 Range R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... 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 (example): Type if a sequence -- DNA, RNA, or amino acid sequence
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:type 0..1 code R5: type
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.type
Binding: sequenceType (required): Type if a sequence -- DNA, RNA, or amino acid sequence.
.... value 0..1 code Primitive value for code
... 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
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:subject 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: Subject this sequence is associated too
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
.... reference ΣC 0..1 string Literal reference, Relative, internal or absolute URL
.... identifier Σ 0..1 Identifier Logical reference, when literal reference is not known
.... display Σ 0..1 string Text alternative for the resource
... specimen Σ 0..1 Reference(Specimen) Specimen used for sequencing
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:specimen 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: specimen additional types
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
.... reference ΣC 0..1 string Literal reference, Relative, internal or absolute URL
.... identifier Σ 0..1 Identifier Logical reference, when literal reference is not known
.... display Σ 0..1 string Text alternative for the resource
... device Σ 0..1 Reference(Device) The method for sequencing
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:device 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: device additional types
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
.... reference ΣC 0..1 string Literal reference, Relative, internal or absolute URL
.... identifier Σ 0..1 Identifier Logical reference, when literal reference is not known
.... display Σ 0..1 string Text alternative for the resource
... performer Σ 0..1 Reference(Organization) Who should be responsible for test result
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:performer 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: performer additional types
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
.... reference ΣC 0..1 string Literal reference, Relative, internal or absolute URL
.... identifier Σ 0..1 Identifier Logical reference, when literal reference is not known
.... display Σ 0..1 string Text alternative for the resource
... quantity Σ 0..1 Quantity The number of copies of the seqeunce of interest. (RNASeq)
... referenceSeq ΣC 0..1 BackboneElement A sequence used as reference
Constraints: seq-4, seq-5, seq-6
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:genomeAssembly 0..1 CodeableConcept R5: The genome assembly used for starting sequence, e.g. GRCh38 (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.genomeAssembly
..... extension:sequence 0..1 CodeableConcept, Reference(Cross-version Profile for R5.MolecularSequence for use in FHIR STU3(0.1.0) | Sequence) R5: The reference sequence that represents the starting sequence additional types
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence
..... extension:orientation 0..1 code R5: sense | antisense (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.orientation
Binding: R5OrientationTypeForR3 (0.1.0) (required): Type for orientation
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored
.... chromosome Σ 0..1 CodeableConcept Chromosome containing genetic finding
Binding: chromosome-human (example): Chromosome number for human
..... id 0..1 string xml:id (or equivalent in JSON)
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
...... extension:chromosome 0..1 CodeableConcept R5: Chromosome Identifier
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome
..... coding Σ 0..* Coding Code defined by a terminology system
..... text Σ 0..1 string Plain text representation of the concept
.... genomeBuild Σ 0..1 string The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
.... referenceSeqId Σ 0..1 CodeableConcept Reference identifier
Binding: ENSEMBL (example): Reference identifier
.... referenceSeqPointer Σ 0..1 Reference(Sequence) A Pointer to another Sequence entity as reference sequence
.... referenceSeqString Σ 0..1 string A string to represent reference sequence
.... strand Σ 0..1 integer Directionality of DNA ( +1/-1)
..... id 0..1 string xml:id (or equivalent in JSON)
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
...... extension:strand 0..1 code R5: watson | crick additional types
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.strand
Binding: R5StrandTypeForR3 (0.1.0) (required): Type for strand
..... value 0..1 integer Primitive value for integer
.... windowStart Σ 1..1 integer Start position of the window on the reference sequence
.... windowEnd Σ 1..1 integer End position of the window on the reference sequence
... variant Σ 0..* BackboneElement Variant in sequence
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:start 0..1 integer R5: Start position of the edit on the starting sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.edit.start
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored
.... 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 xml:id (or equivalent in JSON)
.... extension 0..* Extension Additional Content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored
.... type Σ 1..1 code indel | snp | unknown
Binding: qualityType (required): Type for quality report
.... standardSequence Σ 0..1 CodeableConcept Standard sequence for comparison
Binding: FDA-StandardSequence (example): Reference identifier of the sequence that used to mark the quality of tested samples.
.... 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): The method used to evaluate the numerical quality of the observed sequence.
.... 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
... 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 xml:id (or equivalent in JSON)
.... extension 0..* Extension Additional Content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored
.... type Σ 1..1 code directlink | openapi | login | oauth | other
Binding: repositoryType (required): Type for access of external URI
.... 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(Sequence) Pointer to next atomic sequence

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Sequence.language Base extensible Common Languages . 📍3.0.2 tx.fhir.org
Sequence.type Base example sequenceType 📍3.0.2 FHIR Std.
Sequence.referenceSeq.​chromosome Base example chromosome-human 📍3.0.2 FHIR Std.
Sequence.referenceSeq.​referenceSeqId Base example ENSEMBL 📍3.0.2 FHIR Std.
Sequence.quality.type Base required qualityType 📍3.0.2 FHIR Std.
Sequence.quality.standardSequence Base example FDA-StandardSequence 📍3.0.2 FHIR Std.
Sequence.quality.method Base example FDA-Method 📍3.0.2 FHIR Std.
Sequence.repository.​type Base required repositoryType 📍3.0.2 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dom-1 error Sequence If the resource is contained in another resource, it SHALL NOT contain any narrative contained.text.empty()
dom-2 error Sequence If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Sequence If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource contained.where(('#'+id in %resource.descendants().reference).not()).empty()
dom-4 error Sequence 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()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() | (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
seq-3 error Sequence Only 0 and 1 are valid for coordinateSystem coordinateSystem = 1 or coordinateSystem = 0
seq-4 error Sequence.referenceSeq Only +1 and -1 are valid for strand strand.empty() or strand = 1 or strand = -1
seq-5 error Sequence.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())
seq-6 error Sequence.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

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Sequence C 0..* Sequence Information about a biological sequence
Constraints: seq-3
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:focus 0..* Reference(Cross-version Profile for R5.Resource for use in FHIR STU3(0.1.0) | Resource) R5: What the molecular sequence is about, when it is not about the subject of record (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.focus
.... extension:formatted 0..* Attachment R5: Embedded file or a link (URL) which contains content to represent the sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.formatted
.... extension:coordinateSystem 1..1 CodeableConcept R5: Ways of identifying nucleotides or amino acids within a sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem
.... extension:ordinalPosition 0..1 integer R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition
.... extension:sequenceRange 0..1 Range R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored

doco Documentation for this format

Constraints

Id Grade Path(s) Description Expression
dom-1 error Sequence If the resource is contained in another resource, it SHALL NOT contain any narrative contained.text.empty()
dom-2 error Sequence If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Sequence If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource contained.where(('#'+id in %resource.descendants().reference).not()).empty()
dom-4 error Sequence 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()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() | (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
seq-3 error Sequence Only 0 and 1 are valid for coordinateSystem coordinateSystem = 1 or coordinateSystem = 0

Differential View

This structure is derived from Sequence

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Sequence 0..* Sequence Information about a biological sequence
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:focus 0..* Reference(Cross-version Profile for R5.Resource for use in FHIR STU3(0.1.0) | Resource) R5: What the molecular sequence is about, when it is not about the subject of record (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.focus
.... extension:formatted 0..* Attachment R5: Embedded file or a link (URL) which contains content to represent the sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.formatted
.... extension:coordinateSystem 1..1 CodeableConcept R5: Ways of identifying nucleotides or amino acids within a sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem
.... extension:ordinalPosition 0..1 integer R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition
.... extension:sequenceRange 0..1 Range R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange
... type
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:type 0..1 code R5: type
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.type
Binding: sequenceType (required): Type if a sequence -- DNA, RNA, or amino acid sequence.
... patient
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:subject 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: Subject this sequence is associated too
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:specimen 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: specimen additional types
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
... device
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:device 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: device additional types
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
... performer
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:performer 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: performer additional types
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
... referenceSeq
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:genomeAssembly 0..1 CodeableConcept R5: The genome assembly used for starting sequence, e.g. GRCh38 (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.genomeAssembly
..... extension:sequence 0..1 CodeableConcept, Reference(Cross-version Profile for R5.MolecularSequence for use in FHIR STU3(0.1.0) | Sequence) R5: The reference sequence that represents the starting sequence additional types
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence
..... extension:orientation 0..1 code R5: sense | antisense (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.orientation
Binding: R5OrientationTypeForR3 (0.1.0) (required): Type for orientation
.... chromosome
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
...... extension:chromosome 0..1 CodeableConcept R5: Chromosome Identifier
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome
.... strand
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
...... extension:strand 0..1 code R5: watson | crick additional types
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.strand
Binding: R5StrandTypeForR3 (0.1.0) (required): Type for strand
... variant
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:start 0..1 integer R5: Start position of the edit on the starting sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.edit.start

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Sequence C 0..* Sequence Information about a biological sequence
Constraints: seq-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
... 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
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:focus 0..* Reference(Cross-version Profile for R5.Resource for use in FHIR STU3(0.1.0) | Resource) R5: What the molecular sequence is about, when it is not about the subject of record (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.focus
.... extension:formatted 0..* Attachment R5: Embedded file or a link (URL) which contains content to represent the sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.formatted
.... extension:coordinateSystem 1..1 CodeableConcept R5: Ways of identifying nucleotides or amino acids within a sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem
.... extension:ordinalPosition 0..1 integer R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition
.... extension:sequenceRange 0..1 Range R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... 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 (example): Type if a sequence -- DNA, RNA, or amino acid sequence
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:type 0..1 code R5: type
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.type
Binding: sequenceType (required): Type if a sequence -- DNA, RNA, or amino acid sequence.
.... value 0..1 code Primitive value for code
... 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
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:subject 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: Subject this sequence is associated too
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
.... reference ΣC 0..1 string Literal reference, Relative, internal or absolute URL
.... identifier Σ 0..1 Identifier Logical reference, when literal reference is not known
.... display Σ 0..1 string Text alternative for the resource
... specimen Σ 0..1 Reference(Specimen) Specimen used for sequencing
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:specimen 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: specimen additional types
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
.... reference ΣC 0..1 string Literal reference, Relative, internal or absolute URL
.... identifier Σ 0..1 Identifier Logical reference, when literal reference is not known
.... display Σ 0..1 string Text alternative for the resource
... device Σ 0..1 Reference(Device) The method for sequencing
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:device 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: device additional types
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
.... reference ΣC 0..1 string Literal reference, Relative, internal or absolute URL
.... identifier Σ 0..1 Identifier Logical reference, when literal reference is not known
.... display Σ 0..1 string Text alternative for the resource
... performer Σ 0..1 Reference(Organization) Who should be responsible for test result
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:performer 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: performer additional types
URL: http://hl7.org/fhir/StructureDefinition/alternate-reference
.... reference ΣC 0..1 string Literal reference, Relative, internal or absolute URL
.... identifier Σ 0..1 Identifier Logical reference, when literal reference is not known
.... display Σ 0..1 string Text alternative for the resource
... quantity Σ 0..1 Quantity The number of copies of the seqeunce of interest. (RNASeq)
... referenceSeq ΣC 0..1 BackboneElement A sequence used as reference
Constraints: seq-4, seq-5, seq-6
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:genomeAssembly 0..1 CodeableConcept R5: The genome assembly used for starting sequence, e.g. GRCh38 (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.genomeAssembly
..... extension:sequence 0..1 CodeableConcept, Reference(Cross-version Profile for R5.MolecularSequence for use in FHIR STU3(0.1.0) | Sequence) R5: The reference sequence that represents the starting sequence additional types
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence
..... extension:orientation 0..1 code R5: sense | antisense (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.orientation
Binding: R5OrientationTypeForR3 (0.1.0) (required): Type for orientation
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored
.... chromosome Σ 0..1 CodeableConcept Chromosome containing genetic finding
Binding: chromosome-human (example): Chromosome number for human
..... id 0..1 string xml:id (or equivalent in JSON)
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
...... extension:chromosome 0..1 CodeableConcept R5: Chromosome Identifier
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome
..... coding Σ 0..* Coding Code defined by a terminology system
..... text Σ 0..1 string Plain text representation of the concept
.... genomeBuild Σ 0..1 string The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
.... referenceSeqId Σ 0..1 CodeableConcept Reference identifier
Binding: ENSEMBL (example): Reference identifier
.... referenceSeqPointer Σ 0..1 Reference(Sequence) A Pointer to another Sequence entity as reference sequence
.... referenceSeqString Σ 0..1 string A string to represent reference sequence
.... strand Σ 0..1 integer Directionality of DNA ( +1/-1)
..... id 0..1 string xml:id (or equivalent in JSON)
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
...... extension:strand 0..1 code R5: watson | crick additional types
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.strand
Binding: R5StrandTypeForR3 (0.1.0) (required): Type for strand
..... value 0..1 integer Primitive value for integer
.... windowStart Σ 1..1 integer Start position of the window on the reference sequence
.... windowEnd Σ 1..1 integer End position of the window on the reference sequence
... variant Σ 0..* BackboneElement Variant in sequence
.... id 0..1 string xml:id (or equivalent in JSON)
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:start 0..1 integer R5: Start position of the edit on the starting sequence (new)
URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.edit.start
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored
.... 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 xml:id (or equivalent in JSON)
.... extension 0..* Extension Additional Content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored
.... type Σ 1..1 code indel | snp | unknown
Binding: qualityType (required): Type for quality report
.... standardSequence Σ 0..1 CodeableConcept Standard sequence for comparison
Binding: FDA-StandardSequence (example): Reference identifier of the sequence that used to mark the quality of tested samples.
.... 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): The method used to evaluate the numerical quality of the observed sequence.
.... 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
... 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 xml:id (or equivalent in JSON)
.... extension 0..* Extension Additional Content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored
.... type Σ 1..1 code directlink | openapi | login | oauth | other
Binding: repositoryType (required): Type for access of external URI
.... 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(Sequence) Pointer to next atomic sequence

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Sequence.language Base extensible Common Languages . 📍3.0.2 tx.fhir.org
Sequence.type Base example sequenceType 📍3.0.2 FHIR Std.
Sequence.referenceSeq.​chromosome Base example chromosome-human 📍3.0.2 FHIR Std.
Sequence.referenceSeq.​referenceSeqId Base example ENSEMBL 📍3.0.2 FHIR Std.
Sequence.quality.type Base required qualityType 📍3.0.2 FHIR Std.
Sequence.quality.standardSequence Base example FDA-StandardSequence 📍3.0.2 FHIR Std.
Sequence.quality.method Base example FDA-Method 📍3.0.2 FHIR Std.
Sequence.repository.​type Base required repositoryType 📍3.0.2 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dom-1 error Sequence If the resource is contained in another resource, it SHALL NOT contain any narrative contained.text.empty()
dom-2 error Sequence If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Sequence If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource contained.where(('#'+id in %resource.descendants().reference).not()).empty()
dom-4 error Sequence 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()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() | (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
seq-3 error Sequence Only 0 and 1 are valid for coordinateSystem coordinateSystem = 1 or coordinateSystem = 0
seq-4 error Sequence.referenceSeq Only +1 and -1 are valid for strand strand.empty() or strand = 1 or strand = -1
seq-5 error Sequence.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())
seq-6 error Sequence.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

 

Other representations of profile: CSV, Excel, Schematron