IL Core Implementation Guide
0.18.0 - draft
This page is part of the IL-Core IG (v0.18.0: draft-1 Draft) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version. For a full list of available versions, see the Directory of published versions
Official URL: http://fhir.health.gov.il/StructureDefinition/il-core-molecular-sequence | Version: 0.18.0 | |||
Standards status: Draft | Maturity Level: 0 | Computable Name: ILCoreMolecularSequence |
Israel Core proposed constraints and extensions on the MolecularSequence Resource
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from MolecularSequence
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
MolecularSequence | 0..* | MolecularSequence | ILCore CareTeam Profile | |
patient | 0..1 | Reference(ILCore Patient Profile) | Who and/or what this is about | |
specimen | 0..1 | Reference(ILCore Specimen Profile) | Specimen used for sequencing | |
device | 0..1 | Reference(ILCore Device Profile) | The method for sequencing | |
performer | 0..1 | Reference(ILCore Organization Profile) | Who should be responsible for test result | |
referenceSeq | ||||
referenceSeqPointer | 0..1 | Reference(ILCore Molecular Sequence) | A pointer to another MolecularSequence entity as reference sequence | |
variant | ||||
variantPointer | 0..1 | Reference(ILCore Observation Profile) | Pointer to observed variant information | |
pointer | 0..* | Reference(ILCore Molecular Sequence) | Pointer to next atomic sequence | |
Documentation for this format |
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
MolecularSequence | C | 0..* | MolecularSequence | ILCore CareTeam Profile msq-3: Only 0 and 1 are valid for coordinateSystem |
implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
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(ILCore Patient Profile) | Who and/or what this is about |
specimen | Σ | 0..1 | Reference(ILCore Specimen Profile) | Specimen used for sequencing |
device | Σ | 0..1 | Reference(ILCore Device Profile) | The method for sequencing |
performer | Σ | 0..1 | Reference(ILCore Organization Profile) | Who should be responsible for test result |
pointer | Σ | 0..* | Reference(ILCore Molecular Sequence) | Pointer to next atomic sequence |
Documentation for this format |
Name | Flags | Card. | Type | Description & Constraints | ||||
---|---|---|---|---|---|---|---|---|
MolecularSequence | C | 0..* | MolecularSequence | ILCore CareTeam Profile msq-3: Only 0 and 1 are valid for coordinateSystem | ||||
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 | |||||
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 | 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(ILCore Patient Profile) | Who and/or what this is about | ||||
specimen | Σ | 0..1 | Reference(ILCore Specimen Profile) | Specimen used for sequencing | ||||
device | Σ | 0..1 | Reference(ILCore Device Profile) | The method for sequencing | ||||
performer | Σ | 0..1 | Reference(ILCore Organization Profile) | 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 msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString; | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
chromosome | Σ | 0..1 | CodeableConcept | Chromosome containing genetic finding Binding: chromosome-human (example): Chromosome number for human. | ||||
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(ILCore Molecular Sequence) | A pointer to another MolecularSequence entity as reference sequence | ||||
referenceSeqString | Σ | 0..1 | string | A string to represent reference sequence | ||||
strand | Σ | 0..1 | code | watson | crick Binding: strandType (required): Type for strand. | ||||
windowStart | Σ | 0..1 | integer | Start position of the window on the reference sequence | ||||
windowEnd | Σ | 0..1 | integer | End position of the window on the reference sequence | ||||
variant | Σ | 0..* | BackboneElement | Variant in sequence | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
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(ILCore Observation Profile) | 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 | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
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 | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
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 | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
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(ILCore Molecular Sequence) | 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 | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
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 | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
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 | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
start | Σ | 0..1 | integer | Structural variant inner start | ||||
end | Σ | 0..1 | integer | Structural variant inner end | ||||
Documentation for this format |
Path | Conformance | ValueSet | URI | |||
MolecularSequence.language | preferred | CommonLanguages
http://hl7.org/fhir/ValueSet/languages from the FHIR Standard | ||||
MolecularSequence.type | required | sequenceTypehttp://hl7.org/fhir/ValueSet/sequence-type|4.0.1 from the FHIR Standard | ||||
MolecularSequence.referenceSeq.chromosome | example | chromosome-humanhttp://hl7.org/fhir/ValueSet/chromosome-human from the FHIR Standard | ||||
MolecularSequence.referenceSeq.orientation | required | orientationTypehttp://hl7.org/fhir/ValueSet/orientation-type|4.0.1 from the FHIR Standard | ||||
MolecularSequence.referenceSeq.referenceSeqId | example | ENSEMBLhttp://hl7.org/fhir/ValueSet/sequence-referenceSeq from the FHIR Standard | ||||
MolecularSequence.referenceSeq.strand | required | strandTypehttp://hl7.org/fhir/ValueSet/strand-type|4.0.1 from the FHIR Standard | ||||
MolecularSequence.quality.type | required | qualityTypehttp://hl7.org/fhir/ValueSet/quality-type|4.0.1 from the FHIR Standard | ||||
MolecularSequence.quality.standardSequence | example | FDA-StandardSequence (a valid code from https://precision.fda.gov/files/ )http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence from the FHIR Standard | ||||
MolecularSequence.quality.method | example | FDA-Methodhttp://hl7.org/fhir/ValueSet/sequence-quality-method from the FHIR Standard | ||||
MolecularSequence.repository.type | required | repositoryTypehttp://hl7.org/fhir/ValueSet/repository-type|4.0.1 from the FHIR Standard | ||||
MolecularSequence.structureVariant.variantType | required | LOINC LL379-9|4.0.1http://loinc.org/vs/LL379-9|4.0.1 |
This structure is derived from MolecularSequence
Summary
Structures
This structure refers to these other structures:
Maturity: 0
Differential View
This structure is derived from MolecularSequence
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
MolecularSequence | 0..* | MolecularSequence | ILCore CareTeam Profile | |
patient | 0..1 | Reference(ILCore Patient Profile) | Who and/or what this is about | |
specimen | 0..1 | Reference(ILCore Specimen Profile) | Specimen used for sequencing | |
device | 0..1 | Reference(ILCore Device Profile) | The method for sequencing | |
performer | 0..1 | Reference(ILCore Organization Profile) | Who should be responsible for test result | |
referenceSeq | ||||
referenceSeqPointer | 0..1 | Reference(ILCore Molecular Sequence) | A pointer to another MolecularSequence entity as reference sequence | |
variant | ||||
variantPointer | 0..1 | Reference(ILCore Observation Profile) | Pointer to observed variant information | |
pointer | 0..* | Reference(ILCore Molecular Sequence) | Pointer to next atomic sequence | |
Documentation for this format |
Key Elements View
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
MolecularSequence | C | 0..* | MolecularSequence | ILCore CareTeam Profile msq-3: Only 0 and 1 are valid for coordinateSystem |
implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
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(ILCore Patient Profile) | Who and/or what this is about |
specimen | Σ | 0..1 | Reference(ILCore Specimen Profile) | Specimen used for sequencing |
device | Σ | 0..1 | Reference(ILCore Device Profile) | The method for sequencing |
performer | Σ | 0..1 | Reference(ILCore Organization Profile) | Who should be responsible for test result |
pointer | Σ | 0..* | Reference(ILCore Molecular Sequence) | Pointer to next atomic sequence |
Documentation for this format |
Snapshot View
Name | Flags | Card. | Type | Description & Constraints | ||||
---|---|---|---|---|---|---|---|---|
MolecularSequence | C | 0..* | MolecularSequence | ILCore CareTeam Profile msq-3: Only 0 and 1 are valid for coordinateSystem | ||||
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 | |||||
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 | 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(ILCore Patient Profile) | Who and/or what this is about | ||||
specimen | Σ | 0..1 | Reference(ILCore Specimen Profile) | Specimen used for sequencing | ||||
device | Σ | 0..1 | Reference(ILCore Device Profile) | The method for sequencing | ||||
performer | Σ | 0..1 | Reference(ILCore Organization Profile) | 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 msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString; | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
chromosome | Σ | 0..1 | CodeableConcept | Chromosome containing genetic finding Binding: chromosome-human (example): Chromosome number for human. | ||||
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(ILCore Molecular Sequence) | A pointer to another MolecularSequence entity as reference sequence | ||||
referenceSeqString | Σ | 0..1 | string | A string to represent reference sequence | ||||
strand | Σ | 0..1 | code | watson | crick Binding: strandType (required): Type for strand. | ||||
windowStart | Σ | 0..1 | integer | Start position of the window on the reference sequence | ||||
windowEnd | Σ | 0..1 | integer | End position of the window on the reference sequence | ||||
variant | Σ | 0..* | BackboneElement | Variant in sequence | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
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(ILCore Observation Profile) | 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 | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
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 | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
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 | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
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(ILCore Molecular Sequence) | 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 | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
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 | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
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 | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
start | Σ | 0..1 | integer | Structural variant inner start | ||||
end | Σ | 0..1 | integer | Structural variant inner end | ||||
Documentation for this format |
Path | Conformance | ValueSet | URI | |||
MolecularSequence.language | preferred | CommonLanguages
http://hl7.org/fhir/ValueSet/languages from the FHIR Standard | ||||
MolecularSequence.type | required | sequenceTypehttp://hl7.org/fhir/ValueSet/sequence-type|4.0.1 from the FHIR Standard | ||||
MolecularSequence.referenceSeq.chromosome | example | chromosome-humanhttp://hl7.org/fhir/ValueSet/chromosome-human from the FHIR Standard | ||||
MolecularSequence.referenceSeq.orientation | required | orientationTypehttp://hl7.org/fhir/ValueSet/orientation-type|4.0.1 from the FHIR Standard | ||||
MolecularSequence.referenceSeq.referenceSeqId | example | ENSEMBLhttp://hl7.org/fhir/ValueSet/sequence-referenceSeq from the FHIR Standard | ||||
MolecularSequence.referenceSeq.strand | required | strandTypehttp://hl7.org/fhir/ValueSet/strand-type|4.0.1 from the FHIR Standard | ||||
MolecularSequence.quality.type | required | qualityTypehttp://hl7.org/fhir/ValueSet/quality-type|4.0.1 from the FHIR Standard | ||||
MolecularSequence.quality.standardSequence | example | FDA-StandardSequence (a valid code from https://precision.fda.gov/files/ )http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence from the FHIR Standard | ||||
MolecularSequence.quality.method | example | FDA-Methodhttp://hl7.org/fhir/ValueSet/sequence-quality-method from the FHIR Standard | ||||
MolecularSequence.repository.type | required | repositoryTypehttp://hl7.org/fhir/ValueSet/repository-type|4.0.1 from the FHIR Standard | ||||
MolecularSequence.structureVariant.variantType | required | LOINC LL379-9|4.0.1http://loinc.org/vs/LL379-9|4.0.1 |
This structure is derived from MolecularSequence
Summary
Structures
This structure refers to these other structures:
Maturity: 0
Other representations of profile: CSV, Excel, Schematron