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

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

ConceptMap: R5MolecularSequenceElementMapToR3

Official URL: http://hl7.org/fhir/uv/xver/ConceptMap/R5-MolecularSequence-element-map-to-R3 Version: 0.1.0
Standards status: Trial-use Maturity Level: 0 Computable Name: R5MolecularSequenceElementMapToR3

This ConceptMap represents cross-version mappings for elements from a FHIR R5 MolecularSequence to FHIR STU3.

Mapping from http://hl7.org/fhir/5.0 to http://hl7.org/fhir/3.0


Group 1 Mapping from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0 to http://hl7.org/fhir/StructureDefinition/Sequence|3.0.2

Source Concept DetailsRelationshipTarget Concept DetailsComment
Codes from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0Codes from http://hl7.org/fhir/StructureDefinition/Sequence|3.0.2
MolecularSequence.metameta​is equivalent toSequence.metaSequence.metaElement `MolecularSequence.meta` is mapped to FHIR STU3 element `Sequence.meta` as `Equivalent`.
MolecularSequence.implicitRulesimplicitRules​is equivalent toSequence.implicitRulesSequence.implicitRulesElement `MolecularSequence.implicitRules` is mapped to FHIR STU3 element `Sequence.implicitRules` as `Equivalent`. Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of its narrative along with other profiles, value sets, etc.
MolecularSequence.languagelanguage​is equivalent toSequence.languageSequence.languageElement `MolecularSequence.language` is mapped to FHIR STU3 element `Sequence.language` as `Equivalent`. Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).
MolecularSequence.texttext​is equivalent toSequence.textSequence.textElement `MolecularSequence.text` is mapped to FHIR STU3 element `Sequence.text` as `Equivalent`. Contained resources do not have a narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later.
MolecularSequence.containedcontained​is equivalent toSequence.containedSequence.containedElement `MolecularSequence.contained` is mapped to FHIR STU3 element `Sequence.contained` as `SourceIsBroaderThanTarget`. This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags in their meta elements, but SHALL NOT have security labels.
MolecularSequence.identifieridentifier​is equivalent toSequence.identifierSequence.identifierElement `MolecularSequence.identifier` is mapped to FHIR STU3 element `Sequence.identifier` as `Equivalent`.
MolecularSequence.typetype​maps to wider conceptSequence.typeSequence.typeElement `MolecularSequence.type` is mapped to FHIR STU3 element `Sequence.type` as `Equivalent`.
MolecularSequence.subjectsubject​maps to wider conceptSequence.patientSequence.patientElement `MolecularSequence.subject` is mapped to FHIR STU3 element `Sequence.patient` as `SourceIsBroaderThanTarget`. The standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `MolecularSequence.subject` with unmapped reference targets: BiologicallyDerivedProduct, Group, NutritionProduct, Patient, Substance.
MolecularSequence.specimenspecimen​maps to wider conceptSequence.specimenSequence.specimenElement `MolecularSequence.specimen` is mapped to FHIR STU3 element `Sequence.specimen` as `SourceIsBroaderThanTarget`. The mappings for `MolecularSequence.specimen` do not cover the following types based on type expansion: display, identifier, reference, type. The standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `MolecularSequence.specimen` with unmapped reference targets: Specimen.
MolecularSequence.devicedevice​maps to wider conceptSequence.deviceSequence.deviceElement `MolecularSequence.device` is mapped to FHIR STU3 element `Sequence.device` as `SourceIsBroaderThanTarget`. The mappings for `MolecularSequence.device` do not cover the following types based on type expansion: display, identifier, reference, type. The standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `MolecularSequence.device` with unmapped reference targets: Device.
MolecularSequence.performerperformer​maps to wider conceptSequence.performerSequence.performerElement `MolecularSequence.performer` is mapped to FHIR STU3 element `Sequence.performer` as `SourceIsBroaderThanTarget`. The mappings for `MolecularSequence.performer` do not cover the following types based on type expansion: display, identifier, reference, type. The standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `MolecularSequence.performer` with unmapped reference targets: Organization.
MolecularSequence.literalliteral​is equivalent toSequence.observedSeqSequence.observedSeqElement `MolecularSequence.literal` is mapped to FHIR STU3 element `Sequence.observedSeq` as `Equivalent`.
MolecularSequence.relativerelative​is related toSequence.referenceSeqSequence.referenceSeqElement `MolecularSequence.relative` is mapped to FHIR STU3 element `Sequence.referenceSeq` as `SourceIsBroaderThanTarget`. Element `MolecularSequence.relative` is mapped to FHIR STU3 element `Sequence.variant` as `Equivalent`.
​is related toSequence.variantSequence.variantElement `MolecularSequence.relative` is mapped to FHIR STU3 element `Sequence.referenceSeq` as `SourceIsBroaderThanTarget`. Element `MolecularSequence.relative` is mapped to FHIR STU3 element `Sequence.variant` as `Equivalent`.
MolecularSequence.relative.startingSequencestartingSequence​maps to wider conceptSequence.referenceSeqSequence.referenceSeqElement `MolecularSequence.relative.startingSequence` is mapped to FHIR STU3 element `Sequence.referenceSeq` as `Equivalent`.
MolecularSequence.relative.startingSequence.chromosomechromosome​maps to wider conceptSequence.referenceSeq.chromosomeSequence.referenceSeq.chromosomeElement `MolecularSequence.relative.startingSequence.chromosome` is mapped to FHIR STU3 element `Sequence.referenceSeq.chromosome` as `Equivalent`.
MolecularSequence.relative.startingSequence.sequence[x]sequence[x]​maps to wider conceptSequence.referenceSeq.referenceSeqStringSequence.referenceSeq.referenceSeqStringElement `MolecularSequence.relative.startingSequence.sequence[x]` is mapped to FHIR STU3 element `Sequence.referenceSeq.referenceSeqString` as `SourceIsBroaderThanTarget`. The mappings for `MolecularSequence.relative.startingSequence.sequence[x]` do not cover the following types: CodeableConcept, Reference. A starting sequence may be represented in one of three ways: 1. CodeableConcept, using NCBI, LRG or other appropriate code systems 1. a simple string of IUPAC codes 1. a reference to another MolecularSequence resource.
MolecularSequence.relative.startingSequence.windowStartwindowStart​is equivalent toSequence.referenceSeq.windowStartSequence.referenceSeq.windowStartElement `MolecularSequence.relative.startingSequence.windowStart` is mapped to FHIR STU3 element `Sequence.referenceSeq.windowStart` as `Equivalent`.
MolecularSequence.relative.startingSequence.windowEndwindowEnd​is equivalent toSequence.referenceSeq.windowEndSequence.referenceSeq.windowEndElement `MolecularSequence.relative.startingSequence.windowEnd` is mapped to FHIR STU3 element `Sequence.referenceSeq.windowEnd` as `Equivalent`.
MolecularSequence.relative.startingSequence.strandstrand​maps to wider conceptSequence.referenceSeq.strandSequence.referenceSeq.strandElement `MolecularSequence.relative.startingSequence.strand` is mapped to FHIR STU3 element `Sequence.referenceSeq.strand` as `SourceIsBroaderThanTarget`. The mappings for `MolecularSequence.relative.startingSequence.strand` do not cover the following types: code. The mappings for `MolecularSequence.relative.startingSequence.strand` do not cover the following types based on type expansion: value.
MolecularSequence.relative.editedit​maps to wider conceptSequence.variantSequence.variantElement `MolecularSequence.relative.edit` is mapped to FHIR STU3 element `Sequence.variant` as `Equivalent`.
MolecularSequence.relative.edit.endend​is equivalent toSequence.variant.endSequence.variant.endElement `MolecularSequence.relative.edit.end` is mapped to FHIR STU3 element `Sequence.variant.end` as `Equivalent`.
MolecularSequence.relative.edit.replacementSequencereplacementSequence​is equivalent toSequence.variant.observedAlleleSequence.variant.observedAlleleElement `MolecularSequence.relative.edit.replacementSequence` is mapped to FHIR STU3 element `Sequence.variant.observedAllele` as `Equivalent`.
MolecularSequence.relative.edit.replacedSequencereplacedSequence​is equivalent toSequence.variant.referenceAlleleSequence.variant.referenceAlleleElement `MolecularSequence.relative.edit.replacedSequence` is mapped to FHIR STU3 element `Sequence.variant.referenceAllele` as `Equivalent`.

Group 2 Mapping from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0 to R5: typeversion: 0.1.0)

Source CodeRelationshipTarget CodeComment
MolecularSequence.type (type)​is equivalent toExtension (R5: type)Element `MolecularSequence.type` is mapped to FHIR STU3 element `Sequence.type` as `Equivalent`.

Group 3 Mapping from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0 to R5: What the molecular sequence is about, when it is not about the subject of record (new)version: 0.1.0)

Source CodeRelationshipTarget CodeComment
MolecularSequence.focus (focus)​maps to wider conceptExtension (R5: What the molecular sequence is about, when it is not about the subject of record (new))Element `MolecularSequence.focus` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`. Element `MolecularSequence.focus` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).

Group 4 Mapping from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0 to R5: Embedded file or a link (URL) which contains content to represent the sequence (new)version: 0.1.0)

Source CodeRelationshipTarget CodeComment
MolecularSequence.formatted (formatted)​maps to wider conceptExtension (R5: Embedded file or a link (URL) which contains content to represent the sequence (new))Element `MolecularSequence.formatted` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`. Element `MolecularSequence.formatted` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).

Group 5 Mapping from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0 to R5: Ways of identifying nucleotides or amino acids within a sequence (new)version: 0.1.0)

Source CodeRelationshipTarget CodeComment
MolecularSequence.relative.coordinateSystem (coordinateSystem)​maps to wider conceptExtension (R5: Ways of identifying nucleotides or amino acids within a sequence (new))Element `MolecularSequence.relative.coordinateSystem` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`. Element `MolecularSequence.relative.coordinateSystem` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).

Group 6 Mapping from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0 to R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new)version: 0.1.0)

Source CodeRelationshipTarget CodeComment
MolecularSequence.relative.ordinalPosition (ordinalPosition)​maps to wider conceptExtension (R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new))Element `MolecularSequence.relative.ordinalPosition` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`. Element `MolecularSequence.relative.ordinalPosition` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).

Group 7 Mapping from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0 to R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new)version: 0.1.0)

Source CodeRelationshipTarget CodeComment
MolecularSequence.relative.sequenceRange (sequenceRange)​maps to wider conceptExtension (R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new))Element `MolecularSequence.relative.sequenceRange` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`. Element `MolecularSequence.relative.sequenceRange` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).

Group 8 Mapping from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0 to R5: The genome assembly used for starting sequence, e.g. GRCh38 (new)version: 0.1.0)

Source CodeRelationshipTarget CodeComment
MolecularSequence.relative.startingSequence.genomeAssembly (genomeAssembly)​maps to wider conceptExtension (R5: The genome assembly used for starting sequence, e.g. GRCh38 (new))Element `MolecularSequence.relative.startingSequence.genomeAssembly` has a context of Sequence.referenceSeq based on following the parent source element upwards and mapping to `Sequence`. Element `MolecularSequence.relative.startingSequence.genomeAssembly` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).

Group 9 Mapping from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0 to R5: Chromosome Identifierversion: 0.1.0)

Source CodeRelationshipTarget CodeComment
MolecularSequence.relative.startingSequence.chromosome (chromosome)​is equivalent toExtension (R5: Chromosome Identifier)Element `MolecularSequence.relative.startingSequence.chromosome` is mapped to FHIR STU3 element `Sequence.referenceSeq.chromosome` as `Equivalent`.

Group 10 Mapping from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0 to R5: The reference sequence that represents the starting sequence additional typesversion: 0.1.0)

Source CodeRelationshipTarget CodeComment
MolecularSequence.relative.startingSequence.sequence[x] (sequence[x])​maps to wider conceptExtension (R5: The reference sequence that represents the starting sequence additional types)Element `MolecularSequence.relative.startingSequence.sequence[x]` is mapped to FHIR STU3 element `Sequence.referenceSeq.referenceSeqString` as `SourceIsBroaderThanTarget`. The mappings for `MolecularSequence.relative.startingSequence.sequence[x]` do not cover the following types: CodeableConcept, Reference. A starting sequence may be represented in one of three ways: 1. CodeableConcept, using NCBI, LRG or other appropriate code systems 1. a simple string of IUPAC codes 1. a reference to another MolecularSequence resource.

Group 11 Mapping from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0 to R5: sense | antisense (new)version: 0.1.0)

Source CodeRelationshipTarget CodeComment
MolecularSequence.relative.startingSequence.orientation (orientation)​is equivalent toExtension (R5: sense | antisense (new))Element `MolecularSequence.relative.startingSequence.orientation` has a context of Sequence.referenceSeq based on following the parent source element upwards and mapping to `Sequence`. Element `MolecularSequence.relative.startingSequence.orientation` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).

Group 12 Mapping from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0 to R5: watson | crick additional typesversion: 0.1.0)

Source CodeRelationshipTarget CodeComment
MolecularSequence.relative.startingSequence.strand (strand)​maps to wider conceptExtension (R5: watson | crick additional types)Element `MolecularSequence.relative.startingSequence.strand` is mapped to FHIR STU3 element `Sequence.referenceSeq.strand` as `SourceIsBroaderThanTarget`. The mappings for `MolecularSequence.relative.startingSequence.strand` do not cover the following types: code. The mappings for `MolecularSequence.relative.startingSequence.strand` do not cover the following types based on type expansion: value.

Group 13 Mapping from http://hl7.org/fhir/StructureDefinition/MolecularSequence|5.0.0 to R5: Start position of the edit on the starting sequence (new)version: 0.1.0)

Source CodeRelationshipTarget CodeComment
MolecularSequence.relative.edit.start (start)​maps to wider conceptExtension (R5: Start position of the edit on the starting sequence (new))Element `MolecularSequence.relative.edit.start` has a context of Sequence.variant based on following the parent source element upwards and mapping to `Sequence`. Element `MolecularSequence.relative.edit.start` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).