Extensions for Using Data Elements from FHIR R5 in FHIR R4
0.1.0 - STU
Extensions for Using Data Elements from FHIR R5 in FHIR R4
0.1.0 - STU
Extensions for Using Data Elements from FHIR R5 in FHIR R4 - Downloaded Version null See the Directory of published versions
| Official URL: http://hl7.org/fhir/5.0/StructureDefinition/profile-MolecularSequence | Version: 0.1.0 | |||
| Standards status: Trial-use | Maturity Level: 0 | Computable Name: Profile_R5_MolecularSequence_R4 | ||
This cross-version profile allows R5 MolecularSequence content to be represented via FHIR R4 MolecularSequence resources.
Usages:
You can also check for usages in the FHIR IG Statistics
Description of Profiles, Differentials, Snapshots and how the different presentations work.
| Name | Flags | Card. | Type | Description & Constraints Filter:   |
|---|---|---|---|---|
  MolecularSequence |
C | 0..* | MolecularSequence(4.0.1) | Information about a biological sequence Constraints: msq-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 Constraints: ext-1 | |
   extension:focus |
0..* | Reference(Cross-version Profile for R5.Resource for use in FHIR R4(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 Constraints: ext-1 | |
| 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 Constraints: ext-1 | |
| 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 Constraints: ext-1 | |
| 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 Constraints: ext-1 | |
 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 Constraints: ext-1 | |
 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 | ||||
| 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 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(canonical) = '#').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.extension, MolecularSequence.extension:focus, MolecularSequence.extension:formatted, MolecularSequence.extension:coordinateSystem, MolecularSequence.extension:ordinalPosition, MolecularSequence.extension:sequenceRange, MolecularSequence.modifierExtension, MolecularSequence.coordinateSystem | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | MolecularSequence.extension, MolecularSequence.extension:focus, MolecularSequence.extension:formatted, MolecularSequence.extension:coordinateSystem, MolecularSequence.extension:ordinalPosition, MolecularSequence.extension:sequenceRange, 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: | ||||
|---|---|---|---|---|---|---|---|---|
| MolecularSequence |
C | 0..* | MolecularSequence(4.0.1) | 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): A human language.
| |||||
| 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 Constraints: ext-1 | |||||
| extension:focus |
0..* | Reference(Cross-version Profile for R5.Resource for use in FHIR R4(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 Constraints: ext-1 | |||||
| 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 Constraints: ext-1 | |||||
| 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 Constraints: ext-1 | |||||
| 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 Constraints: ext-1 | |||||
| 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 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 | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url Constraints: ext-1 | |||||
| extension:subject |
0..1 | Reference(Resource) | R5: Subject this sequence is associated too URL: http://hl7.org/fhir/StructureDefinition/alternate-reference Constraints: ext-1 | |||||
| reference |
ΣC | 0..1 | string | Literal reference, Relative, internal or absolute URL | ||||
| type |
Σ | 0..1 | uri | Type the reference refers to (e.g. "Patient") Binding: ResourceType (extensible): Aa resource (or, for logical models, the URI of the logical model). | ||||
| 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 | ||||
| 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 | |||||
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url Constraints: ext-1 | |||||
| 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 Constraints: ext-1 | |||||
| extension:sequence |
0..1 | CodeableConcept, Reference(Cross-version Profile for R5.MolecularSequence for use in FHIR R4(0.1.0) | MolecularSequence) | R5: The reference sequence that represents the starting sequence additional types URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence 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): Chromosome number for human. | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url Constraints: ext-1 | |||||
| extension:chromosome |
0..1 | CodeableConcept | R5: Chromosome Identifier URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome Constraints: ext-1 | |||||
| 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' | ||||
| 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. | ||||
| 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 | |||||
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url Constraints: ext-1 | |||||
| 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 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 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 | ||||
 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 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(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|4.0.1 (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 | ||||||||
| Path | Status | Usage | ValueSet | Version | Source |
| MolecularSequence.language | Base | preferred |
Common Languages
|
📍4.0.1 | tx.fhir.org |
| MolecularSequence.type | Base | required | sequenceType | 📍4.0.1 | FHIR Std. |
| MolecularSequence.patient.type | Base | extensible |
ResourceType
|
📍4.0.1 | tx.fhir.org |
| MolecularSequence.referenceSeq.chromosome | Base | example | chromosome-human | 📍4.0.1 | FHIR Std. |
| MolecularSequence.referenceSeq.orientation | Base | required | orientationType | 📍4.0.1 | FHIR Std. |
| MolecularSequence.referenceSeq.referenceSeqId | Base | example | E n s e m b l | 📍4.0.1 | FHIR Std. |
| MolecularSequence.referenceSeq.strand | Base | required | strandType | 📍4.0.1 | FHIR Std. |
| MolecularSequence.quality.type | Base | required | qualityType | 📍4.0.1 | FHIR Std. |
| MolecularSequence.quality.standardSequence | Base | example | F d a- standard sequence | 📍4.0.1 | FHIR Std. |
| MolecularSequence.quality.method | Base | example | F d a- method | 📍4.0.1 | FHIR Std. |
| MolecularSequence.repository.type | Base | required | repositoryType | 📍4.0.1 | FHIR Std. |
| MolecularSequence.structureVariant.variantType | Base | required | LOINC Answer Codes for LL379-9|4.0.1 | 📍4.0.1 | unknown? |
| 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 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(canonical) = '#').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.meta, MolecularSequence.implicitRules, MolecularSequence.language, MolecularSequence.text, MolecularSequence.extension, MolecularSequence.extension:focus, MolecularSequence.extension:formatted, MolecularSequence.extension:coordinateSystem, MolecularSequence.extension:ordinalPosition, MolecularSequence.extension:sequenceRange, MolecularSequence.modifierExtension, MolecularSequence.identifier, MolecularSequence.type, MolecularSequence.coordinateSystem, MolecularSequence.patient, MolecularSequence.patient.extension, MolecularSequence.patient.extension:subject, MolecularSequence.patient.reference, MolecularSequence.patient.type, MolecularSequence.patient.identifier, MolecularSequence.patient.display, MolecularSequence.specimen, MolecularSequence.device, MolecularSequence.performer, MolecularSequence.quantity, MolecularSequence.referenceSeq, MolecularSequence.referenceSeq.extension, MolecularSequence.referenceSeq.extension:genomeAssembly, MolecularSequence.referenceSeq.extension:sequence, MolecularSequence.referenceSeq.modifierExtension, MolecularSequence.referenceSeq.chromosome, MolecularSequence.referenceSeq.chromosome.extension, MolecularSequence.referenceSeq.chromosome.extension:chromosome, MolecularSequence.referenceSeq.chromosome.coding, MolecularSequence.referenceSeq.chromosome.text, 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.extension:start, 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.extension:focus, MolecularSequence.extension:formatted, MolecularSequence.extension:coordinateSystem, MolecularSequence.extension:ordinalPosition, MolecularSequence.extension:sequenceRange, MolecularSequence.modifierExtension, MolecularSequence.patient.extension, MolecularSequence.patient.extension:subject, MolecularSequence.referenceSeq.extension, MolecularSequence.referenceSeq.extension:genomeAssembly, MolecularSequence.referenceSeq.extension:sequence, MolecularSequence.referenceSeq.modifierExtension, MolecularSequence.referenceSeq.chromosome.extension, MolecularSequence.referenceSeq.chromosome.extension:chromosome, MolecularSequence.variant.extension, MolecularSequence.variant.extension:start, 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
Mandatory: 2 elements
Extensions
This structure refers to these extensions:
Maturity: 0
Key Elements View
| Name | Flags | Card. | Type | Description & Constraints Filter: |
|---|---|---|---|---|
| MolecularSequence |
C | 0..* | MolecularSequence(4.0.1) | Information about a biological sequence Constraints: msq-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 Constraints: ext-1 | |
| extension:focus |
0..* | Reference(Cross-version Profile for R5.Resource for use in FHIR R4(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 Constraints: ext-1 | |
| 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 Constraints: ext-1 | |
| 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 Constraints: ext-1 | |
| 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 Constraints: ext-1 | |
| 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 Constraints: ext-1 | |
| 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 | ||||
| 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 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(canonical) = '#').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.extension, MolecularSequence.extension:focus, MolecularSequence.extension:formatted, MolecularSequence.extension:coordinateSystem, MolecularSequence.extension:ordinalPosition, MolecularSequence.extension:sequenceRange, MolecularSequence.modifierExtension, MolecularSequence.coordinateSystem | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | MolecularSequence.extension, MolecularSequence.extension:focus, MolecularSequence.extension:formatted, MolecularSequence.extension:coordinateSystem, MolecularSequence.extension:ordinalPosition, MolecularSequence.extension:sequenceRange, 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
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints Filter: | ||||
|---|---|---|---|---|---|---|---|---|
| MolecularSequence |
C | 0..* | MolecularSequence(4.0.1) | 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): A human language.
| |||||
| 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 Constraints: ext-1 | |||||
| extension:focus |
0..* | Reference(Cross-version Profile for R5.Resource for use in FHIR R4(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 Constraints: ext-1 | |||||
| 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 Constraints: ext-1 | |||||
| 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 Constraints: ext-1 | |||||
| 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 Constraints: ext-1 | |||||
| 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 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 | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url Constraints: ext-1 | |||||
| extension:subject |
0..1 | Reference(Resource) | R5: Subject this sequence is associated too URL: http://hl7.org/fhir/StructureDefinition/alternate-reference Constraints: ext-1 | |||||
| reference |
ΣC | 0..1 | string | Literal reference, Relative, internal or absolute URL | ||||
| type |
Σ | 0..1 | uri | Type the reference refers to (e.g. "Patient") Binding: ResourceType (extensible): Aa resource (or, for logical models, the URI of the logical model). | ||||
| 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 | ||||
| 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 | |||||
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url Constraints: ext-1 | |||||
| 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 Constraints: ext-1 | |||||
| extension:sequence |
0..1 | CodeableConcept, Reference(Cross-version Profile for R5.MolecularSequence for use in FHIR R4(0.1.0) | MolecularSequence) | R5: The reference sequence that represents the starting sequence additional types URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence 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): Chromosome number for human. | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url Constraints: ext-1 | |||||
| extension:chromosome |
0..1 | CodeableConcept | R5: Chromosome Identifier URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome Constraints: ext-1 | |||||
| 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' | ||||
| 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. | ||||
| 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 | |||||
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url Constraints: ext-1 | |||||
| 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 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 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 | ||||
| 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 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(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|4.0.1 (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 | ||||||||
| Path | Status | Usage | ValueSet | Version | Source |
| MolecularSequence.language | Base | preferred |
Common Languages
|
📍4.0.1 | tx.fhir.org |
| MolecularSequence.type | Base | required | sequenceType | 📍4.0.1 | FHIR Std. |
| MolecularSequence.patient.type | Base | extensible |
ResourceType
|
📍4.0.1 | tx.fhir.org |
| MolecularSequence.referenceSeq.chromosome | Base | example | chromosome-human | 📍4.0.1 | FHIR Std. |
| MolecularSequence.referenceSeq.orientation | Base | required | orientationType | 📍4.0.1 | FHIR Std. |
| MolecularSequence.referenceSeq.referenceSeqId | Base | example | E n s e m b l | 📍4.0.1 | FHIR Std. |
| MolecularSequence.referenceSeq.strand | Base | required | strandType | 📍4.0.1 | FHIR Std. |
| MolecularSequence.quality.type | Base | required | qualityType | 📍4.0.1 | FHIR Std. |
| MolecularSequence.quality.standardSequence | Base | example | F d a- standard sequence | 📍4.0.1 | FHIR Std. |
| MolecularSequence.quality.method | Base | example | F d a- method | 📍4.0.1 | FHIR Std. |
| MolecularSequence.repository.type | Base | required | repositoryType | 📍4.0.1 | FHIR Std. |
| MolecularSequence.structureVariant.variantType | Base | required | LOINC Answer Codes for LL379-9|4.0.1 | 📍4.0.1 | unknown? |
| 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 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(canonical) = '#').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.meta, MolecularSequence.implicitRules, MolecularSequence.language, MolecularSequence.text, MolecularSequence.extension, MolecularSequence.extension:focus, MolecularSequence.extension:formatted, MolecularSequence.extension:coordinateSystem, MolecularSequence.extension:ordinalPosition, MolecularSequence.extension:sequenceRange, MolecularSequence.modifierExtension, MolecularSequence.identifier, MolecularSequence.type, MolecularSequence.coordinateSystem, MolecularSequence.patient, MolecularSequence.patient.extension, MolecularSequence.patient.extension:subject, MolecularSequence.patient.reference, MolecularSequence.patient.type, MolecularSequence.patient.identifier, MolecularSequence.patient.display, MolecularSequence.specimen, MolecularSequence.device, MolecularSequence.performer, MolecularSequence.quantity, MolecularSequence.referenceSeq, MolecularSequence.referenceSeq.extension, MolecularSequence.referenceSeq.extension:genomeAssembly, MolecularSequence.referenceSeq.extension:sequence, MolecularSequence.referenceSeq.modifierExtension, MolecularSequence.referenceSeq.chromosome, MolecularSequence.referenceSeq.chromosome.extension, MolecularSequence.referenceSeq.chromosome.extension:chromosome, MolecularSequence.referenceSeq.chromosome.coding, MolecularSequence.referenceSeq.chromosome.text, 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.extension:start, 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.extension:focus, MolecularSequence.extension:formatted, MolecularSequence.extension:coordinateSystem, MolecularSequence.extension:ordinalPosition, MolecularSequence.extension:sequenceRange, MolecularSequence.modifierExtension, MolecularSequence.patient.extension, MolecularSequence.patient.extension:subject, MolecularSequence.referenceSeq.extension, MolecularSequence.referenceSeq.extension:genomeAssembly, MolecularSequence.referenceSeq.extension:sequence, MolecularSequence.referenceSeq.modifierExtension, MolecularSequence.referenceSeq.chromosome.extension, MolecularSequence.referenceSeq.chromosome.extension:chromosome, MolecularSequence.variant.extension, MolecularSequence.variant.extension:start, 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
Mandatory: 2 elements
Extensions
This structure refers to these extensions:
Maturity: 0
Other representations of profile: CSV, Excel, Schematron
IG © 2025+ FHIR Infrastructure. Package hl7.fhir.uv.xver-r5.r4#0.1.0 based on FHIR 4.0.1. Generated 2026-03-20
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