This page is part of the Genetic Reporting Implementation Guide (v0.1.0: STU 1 Ballot 1) based on FHIR v3.3.0. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
The official URL for this profile is:
http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from Sequence
This structure is derived from Sequence
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Sequence | 0..* | Definitional Sequence | ||
 type | S | 1..1 | code | |
| coordinateSystem | S | 1..1 | integer | |
| patient | 0..0 | |||
| specimen | 0..0 | |||
| device | 0..0 | |||
| performer | 0..0 | |||
| referenceSeq | S | 0..1 | BackboneElement | |
  genomeBuild | S | 0..1 | string | |
| variant | 0..0 | |||
| quality | 0..0 | |||
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Sequence | I | 0..* | Definitional Sequence | |
 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: Common Languages (extensible) | |
| text | I | 0..1 | Narrative | Text summary of the resource, for human interpretation |
 contained | 0..* | Resource | Contained, inline Resources | |
 extension | 0..* | Extension | Additional Content defined by implementations | |
 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 | SΣ | 1..1 | code | aa | dna | rna Binding: sequenceType (example) |
| coordinateSystem | SΣ | 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) |
| quantity | Σ | 0..1 | Quantity | The number of copies of the seqeunce of interest. (RNASeq) |
| referenceSeq | SΣI | 0..1 | BackboneElement | A sequence used as reference |
| 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 |
| chromosome | Σ | 0..1 | CodeableConcept | Chromosome containing genetic finding Binding: chromosome-human (example) |
| genomeBuild | SΣ | 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) |
| referenceSeqId | Σ | 0..1 | CodeableConcept | Reference identifier Binding: ENSEMBL (example) |
 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 | code | watson | crick Binding: strandType (required) |
| 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 |
| observedSeq | Σ | 0..1 | string | Sequence that was observed |
| readCoverage | Σ | 0..1 | integer | Average number of reads representing a given nucleotide in the reconstructed sequence |
| repository | ΣI | 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) |
| 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 |
| structureVariant | ΣI | 0..* | BackboneElement | Structural variant |
 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 |
| precision | Σ | 0..1 | string | Precision of boundaries |
| reportedaCGHRatio | Σ | 0..1 | decimal | Structural Variant reported aCGH ratio |
| length | Σ | 0..1 | integer | Structural Variant Length |
| outer | ΣI | 0..1 | BackboneElement | Structural variant outer |
| 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 |
| start | Σ | 0..1 | integer | Structural Variant Outer Start |
| end | Σ | 0..1 | integer | Structural Variant Outer End |
| inner | ΣI | 0..1 | BackboneElement | Structural variant inner |
| 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 |
| start | Σ | 0..1 | integer | Structural Variant Inner Start |
| end | Σ | 0..1 | integer | Structural Variant Inner End |
| Documentation for this format | ||||
This structure is derived from Sequence
Differential View
This structure is derived from Sequence
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Sequence | 0..* | Definitional Sequence | ||
| type | S | 1..1 | code | |
| coordinateSystem | S | 1..1 | integer | |
| patient | 0..0 | |||
| specimen | 0..0 | |||
| device | 0..0 | |||
| performer | 0..0 | |||
| referenceSeq | S | 0..1 | BackboneElement | |
| genomeBuild | S | 0..1 | string | |
| variant | 0..0 | |||
| quality | 0..0 | |||
| Documentation for this format | ||||
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Sequence | I | 0..* | Definitional Sequence | |
| 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: Common Languages (extensible) | |
| text | I | 0..1 | Narrative | Text summary of the resource, for human interpretation |
| contained | 0..* | Resource | Contained, inline Resources | |
| extension | 0..* | Extension | Additional Content defined by implementations | |
| 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 | SΣ | 1..1 | code | aa | dna | rna Binding: sequenceType (example) |
| coordinateSystem | SΣ | 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) |
| quantity | Σ | 0..1 | Quantity | The number of copies of the seqeunce of interest. (RNASeq) |
| referenceSeq | SΣI | 0..1 | BackboneElement | A sequence used as reference |
| 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 |
| chromosome | Σ | 0..1 | CodeableConcept | Chromosome containing genetic finding Binding: chromosome-human (example) |
| genomeBuild | SΣ | 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) |
| referenceSeqId | Σ | 0..1 | CodeableConcept | Reference identifier Binding: ENSEMBL (example) |
| 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 | code | watson | crick Binding: strandType (required) |
| 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 |
| observedSeq | Σ | 0..1 | string | Sequence that was observed |
| readCoverage | Σ | 0..1 | integer | Average number of reads representing a given nucleotide in the reconstructed sequence |
| repository | ΣI | 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) |
| 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 |
| structureVariant | ΣI | 0..* | BackboneElement | Structural variant |
| 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 |
| precision | Σ | 0..1 | string | Precision of boundaries |
| reportedaCGHRatio | Σ | 0..1 | decimal | Structural Variant reported aCGH ratio |
| length | Σ | 0..1 | integer | Structural Variant Length |
| outer | ΣI | 0..1 | BackboneElement | Structural variant outer |
| 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 |
| start | Σ | 0..1 | integer | Structural Variant Outer Start |
| end | Σ | 0..1 | integer | Structural Variant Outer End |
| inner | ΣI | 0..1 | BackboneElement | Structural variant inner |
| 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 |
| start | Σ | 0..1 | integer | Structural Variant Inner Start |
| end | Σ | 0..1 | integer | Structural Variant Inner End |
| Documentation for this format | ||||
Other representations of profile: Schematron
| Path | Name | Conformance | ValueSet |
| Sequence.language | Common Languages | extensible | Common Languages |
| Sequence.type | sequenceType | example | sequenceType |
| Sequence.referenceSeq.chromosome | chromosome-human | example | chromosome-human |
| Sequence.referenceSeq.orientation | orientationType | required | orientationType |
| Sequence.referenceSeq.referenceSeqId | ENSEMBL | example | ENSEMBL |
| Sequence.referenceSeq.strand | strandType | required | strandType |
| Sequence.quality.type | qualityType | required | qualityType |
| Sequence.quality.standardSequence | FDA-StandardSequence | example | FDA-StandardSequence |
| Sequence.quality.method | FDA-Method | example | FDA-Method |
| Sequence.repository.type | repositoryType | required | repositoryType |
| Id | Path | Details | Requirements |
| dom-2 | Sequence | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-1 | Sequence | If the resource is contained in another resource, it SHALL NOT contain any narrative : contained.text.empty() | |
| dom-4 | 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() | |
| dom-3 | Sequence | 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.all(('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists()) | |
| seq-3 | Sequence | Only 0 and 1 are valid for coordinateSystem : coordinateSystem = 1 or coordinateSystem = 0 | |
| ele-1 | Sequence.referenceSeq | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
| seq-5 | 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 | 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 | |
| ele-1 | Sequence.quality.roc | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
| ele-1 | Sequence.repository | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
| ele-1 | Sequence.structureVariant | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
| ele-1 | Sequence.structureVariant.outer | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
| ele-1 | Sequence.structureVariant.inner | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) |
© 2017+ HL7 International Clinical Genomics Work Group. Based on FHIR version (3.3.0-13671). IG generated on Wed, Apr 4, 2018 06:23+1000.
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