IL Core Implementation Guide
0.18.0 - draft Israel flag

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

Resource Profile: ILCore Molecular Sequence

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:

Formal Views of Profile Content

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

This structure is derived from MolecularSequence

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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
... 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

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. 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)
... 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

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. 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
... 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
MolecularSequence.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
MolecularSequence.typerequiredsequenceType
http://hl7.org/fhir/ValueSet/sequence-type|4.0.1
from the FHIR Standard
MolecularSequence.referenceSeq.chromosomeexamplechromosome-human
http://hl7.org/fhir/ValueSet/chromosome-human
from the FHIR Standard
MolecularSequence.referenceSeq.orientationrequiredorientationType
http://hl7.org/fhir/ValueSet/orientation-type|4.0.1
from the FHIR Standard
MolecularSequence.referenceSeq.referenceSeqIdexampleENSEMBL
http://hl7.org/fhir/ValueSet/sequence-referenceSeq
from the FHIR Standard
MolecularSequence.referenceSeq.strandrequiredstrandType
http://hl7.org/fhir/ValueSet/strand-type|4.0.1
from the FHIR Standard
MolecularSequence.quality.typerequiredqualityType
http://hl7.org/fhir/ValueSet/quality-type|4.0.1
from the FHIR Standard
MolecularSequence.quality.standardSequenceexampleFDA-StandardSequence (a valid code from https://precision.fda.gov/files/)
http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence
from the FHIR Standard
MolecularSequence.quality.methodexampleFDA-Method
http://hl7.org/fhir/ValueSet/sequence-quality-method
from the FHIR Standard
MolecularSequence.repository.typerequiredrepositoryType
http://hl7.org/fhir/ValueSet/repository-type|4.0.1
from the FHIR Standard
MolecularSequence.structureVariant.variantTyperequiredLOINC LL379-9|4.0.1
http://loinc.org/vs/LL379-9|4.0.1

Differential View

This structure is derived from MolecularSequence

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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
... 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

doco Documentation for this format

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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)
... 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

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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
... 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
MolecularSequence.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
MolecularSequence.typerequiredsequenceType
http://hl7.org/fhir/ValueSet/sequence-type|4.0.1
from the FHIR Standard
MolecularSequence.referenceSeq.chromosomeexamplechromosome-human
http://hl7.org/fhir/ValueSet/chromosome-human
from the FHIR Standard
MolecularSequence.referenceSeq.orientationrequiredorientationType
http://hl7.org/fhir/ValueSet/orientation-type|4.0.1
from the FHIR Standard
MolecularSequence.referenceSeq.referenceSeqIdexampleENSEMBL
http://hl7.org/fhir/ValueSet/sequence-referenceSeq
from the FHIR Standard
MolecularSequence.referenceSeq.strandrequiredstrandType
http://hl7.org/fhir/ValueSet/strand-type|4.0.1
from the FHIR Standard
MolecularSequence.quality.typerequiredqualityType
http://hl7.org/fhir/ValueSet/quality-type|4.0.1
from the FHIR Standard
MolecularSequence.quality.standardSequenceexampleFDA-StandardSequence (a valid code from https://precision.fda.gov/files/)
http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence
from the FHIR Standard
MolecularSequence.quality.methodexampleFDA-Method
http://hl7.org/fhir/ValueSet/sequence-quality-method
from the FHIR Standard
MolecularSequence.repository.typerequiredrepositoryType
http://hl7.org/fhir/ValueSet/repository-type|4.0.1
from the FHIR Standard
MolecularSequence.structureVariant.variantTyperequiredLOINC LL379-9|4.0.1
http://loinc.org/vs/LL379-9|4.0.1

 

Other representations of profile: CSV, Excel, Schematron