This is the Continuous Integration Build of FHIR (will be incorrect/inconsistent at times).
See the Directory of published versions
Clinical Genomics Work Group | Maturity Level: 0 | Trial Use | Security Category: N/A | Compartments: No defined compartments |
Representation of a molecular definition.
Note to Implementers: Molecular Definition resource will replace Molecular Sequence resource. Current page of the Molecular Sequence is temporarily available for referencing and review purposes.
The MoleculerDefinition resource is designed for representing genetic molecules (e.g., sequence). It can represent the genetic molecules in different ways, allowing implementations to adopt the most effective ones for their use cases.
The MoleculerDefinition resource is designed to represent a single sequence or a composite of genetic sequences (e.g., haplotype). Each genetic molecule might have multiple representations, but implementers SHALL ensure all representations are for the same molecule. This means that if a single MoleculerDefinition instance contains a literal
, two formatted
files, and a relative
, all four of those representations must represent the same genetic molecule (e.g.,sequence). This can be a challenge across systems, as semantic equivalency of sequences cannot be guaranteed unless there is an agreed upon standard between sending and receiving systems.
The MoleculerDefinition resource should only be used to capture molecular representations of genetic concepts such as sequence, allele, and haplotype. It will not be used for observational data related to specific patient. Those concepts will be captured in Observation profiles found in the Genomics Reporting Implementation Guide . The molecule that was observed and that led to the identification of those concepts can be delivered with this resource, and will be referenced by those observations.
MoleculerDefinition will not be used to capture data such as precise read of DNA sequences and sequence alignment are not included; such data may be accessible through references to GA4GH (Global Alliance for Genomics and Health) API, and may be referenced to by the literal
element.
Structure
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
MolecularDefinition | TU | DomainResource | Representation of a molecular definition Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension | |
identifier | Σ | 0..* | Identifier | Unique ID for this particular resource |
type | Σ | 0..1 | code | aa | dna | rna Binding: sequence Type (Required) |
location | Σ | 0..* | BackboneElement | Location of this molecule |
sequenceLocation | Σ | 0..1 | BackboneElement | Location of this molecule in context of a sequence |
sequenceContext | Σ | 1..1 | Reference(MolecularDefinition) | Reference sequence |
coordinateInterval | Σ | 0..1 | BackboneElement | Coordinate Interval for this location |
numberingSystem | Σ | 0..1 | CodeableConcept | Coordinate System |
start[x] | Σ | 0..1 | Start | |
startQuantity | Quantity | |||
startRange | Range | |||
end[x] | Σ | 0..1 | End | |
endQuantity | Quantity | |||
endRange | Range | |||
strand | 0..1 | CodeableConcept | Forward or Reverse | |
cytobandLocation | Σ | 0..1 | BackboneElement | Location of this molecule in context of a cytoband |
genomeAssembly | Σ | 1..1 | BackboneElement | Reference Genome |
organism | 0..1 | CodeableConcept | Species of the organism | |
build | 0..1 | CodeableConcept | Build number | |
accession | 0..1 | CodeableConcept | Accession | |
description[x] | 0..1 | Genome assemble description | ||
descriptionMarkdown | markdown | |||
descriptionString | string | |||
cytobandInterval | Σ | 1..1 | BackboneElement | Cytoband Interval |
chromosome | Σ | 1..1 | CodeableConcept | Chromosome |
startCytoband | Σ | 0..1 | BackboneElement | Start |
arm[x] | 0..1 | Arm | ||
armCode | code | |||
armString | string | |||
region[x] | 0..1 | Region | ||
regionCode | code | |||
regionString | string | |||
band[x] | 0..1 | Band | ||
bandCode | code | |||
bandString | string | |||
subBand[x] | 0..1 | Sub-band | ||
subBandCode | code | |||
subBandString | string | |||
endCytoband | Σ | 0..1 | BackboneElement | End |
arm[x] | 0..1 | Arm | ||
armCode | code | |||
armString | string | |||
region[x] | 0..1 | Region | ||
regionCode | code | |||
regionString | string | |||
band[x] | 0..1 | Band | ||
bandCode | code | |||
bandString | string | |||
subBand[x] | 0..1 | SuBand | ||
subBandCode | code | |||
subBandString | string | |||
featureLocation | Σ | 0..* | BackboneElement | Location in context of a feature |
geneId | Σ | 0..* | CodeableConcept | Gene Id |
memberState | Σ | 0..* | Reference(MolecularDefinition) | Member |
representation | Σ | 0..* | BackboneElement | Representation |
focus | Σ | 0..1 | CodeableConcept | The focus of the representation |
code | Σ | 0..* | CodeableConcept | A code of the representation |
literal | Σ | 0..1 | BackboneElement | A literal representation |
encoding | Σ | 0..1 | CodeableConcept | The encoding used for the expression of the primary sequence |
value | Σ | 1..1 | string | The primary (linear) sequence, expressed as a literal string |
resolvable | Σ | 0..1 | Attachment | A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself |
extracted | Σ | 0..1 | BackboneElement | A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence |
startingMolecule | Σ | 1..1 | Reference(MolecularDefinition) | The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted |
start | Σ | 1..1 | integer | The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted |
end | Σ | 1..1 | integer | The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted |
coordinateSystem | Σ | 1..1 | CodeableConcept | The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based |
reverseComplement | Σ | 0..1 | boolean | A flag that indicates whether the extracted sequence should be reverse complemented |
repeated | Σ | 0..1 | BackboneElement | A Molecular Sequence that is represented as a repeated sequence motif |
sequenceMotif | Σ | 1..1 | Reference(MolecularDefinition) | The sequence that defines the repeated motif |
copyCount | Σ | 1..1 | integer | The number of repeats (copies) of the sequence motif |
concatenated | Σ | 0..1 | BackboneElement | A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences |
sequenceElement | Σ | 1..* | BackboneElement | One element of a concatenated Molecular Sequence |
sequence | Σ | 1..1 | Reference(MolecularDefinition) | The Molecular Sequence corresponding to this element |
ordinalIndex | Σ | 1..1 | integer | The ordinal position of this sequence element within the concatenated Molecular Sequence |
relative | Σ | 0..1 | BackboneElement | A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence |
startingMolecule | Σ | 1..1 | Reference(MolecularDefinition) | The Molecular Sequence that serves as the starting sequence, on which edits will be applied |
edit | Σ | 0..* | BackboneElement | An edit (change) made to a sequence |
editOrder | 0..1 | integer | The order of this edit, relative to other edits on the starting sequence | |
coordinateSystem | Σ | 1..1 | CodeableConcept | The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based Binding: LL5323-2 (Extensible) |
start | Σ | 1..1 | integer | The start coordinate of the interval that will be edited |
end | Σ | 1..1 | integer | The end coordinate of the interval that will be edited |
replacementMolecule | Σ | 1..1 | Reference(MolecularDefinition) | The sequence that defines the replacement sequence used in the edit operation |
replacedMolecule | Σ | 0..1 | Reference(MolecularDefinition) | The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit |
Documentation for this format |
See the Extensions for this resource
UML Diagram (Legend)
XML Template
<MolecularDefinition xmlns="http://hl7.org/fhir"> <!-- from Resource: id, meta, implicitRules, and language --> <!-- from DomainResource: text, contained, extension, and modifierExtension --> <identifier><!-- 0..* Identifier Unique ID for this particular resource --></identifier> <type value="[code]"/><!-- 0..1 aa | dna | rna --> <location> <!-- 0..* Location of this molecule --> <sequenceLocation> <!-- 0..1 Location of this molecule in context of a sequence --> <sequenceContext><!-- 1..1 Reference(MolecularDefinition) Reference sequence --></sequenceContext> <coordinateInterval> <!-- 0..1 Coordinate Interval for this location --> <numberingSystem><!-- 0..1 CodeableConcept Coordinate System --></numberingSystem> <start[x]><!-- 0..1 Quantity|Range Start --></start[x]> <end[x]><!-- 0..1 Quantity|Range End --></end[x]> </coordinateInterval> <strand><!-- 0..1 CodeableConcept Forward or Reverse --></strand> </sequenceLocation> <cytobandLocation> <!-- 0..1 Location of this molecule in context of a cytoband --> <genomeAssembly> <!-- 1..1 Reference Genome --> <organism><!-- 0..1 CodeableConcept Species of the organism --></organism> <build><!-- 0..1 CodeableConcept Build number --></build> <accession><!-- 0..1 CodeableConcept Accession --></accession> <description[x]><!-- 0..1 markdown|string Genome assemble description --></description[x]> </genomeAssembly> <cytobandInterval> <!-- 1..1 Cytoband Interval --> <chromosome><!-- 1..1 CodeableConcept Chromosome --></chromosome> <startCytoband> <!-- 0..1 Start --> <arm[x]><!-- 0..1 code|string Arm --></arm[x]> <region[x]><!-- 0..1 code|string Region --></region[x]> <band[x]><!-- 0..1 code|string Band --></band[x]> <subBand[x]><!-- 0..1 code|string Sub-band --></subBand[x]> </startCytoband> <endCytoband> <!-- 0..1 End --> <arm[x]><!-- 0..1 code|string Arm --></arm[x]> <region[x]><!-- 0..1 code|string Region --></region[x]> <band[x]><!-- 0..1 code|string Band --></band[x]> <subBand[x]><!-- 0..1 code|string SuBand --></subBand[x]> </endCytoband> </cytobandInterval> </cytobandLocation> <featureLocation> <!-- 0..* Location in context of a feature --> <geneId><!-- 0..* CodeableConcept Gene Id --></geneId> </featureLocation> </location> <memberState><!-- 0..* Reference(MolecularDefinition) Member --></memberState> <representation> <!-- 0..* Representation --> <focus><!-- 0..1 CodeableConcept The focus of the representation --></focus> <code><!-- 0..* CodeableConcept A code of the representation --></code> <literal> <!-- 0..1 A literal representation --> <encoding><!-- 0..1 CodeableConcept The encoding used for the expression of the primary sequence --></encoding> <value value="[string]"/><!-- 1..1 The primary (linear) sequence, expressed as a literal string --> </literal> <resolvable><!-- 0..1 Attachment A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself --></resolvable> <extracted> <!-- 0..1 A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence --> <startingMolecule><!-- 1..1 Reference(MolecularDefinition) The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted --></startingMolecule> <start value="[integer]"/><!-- 1..1 The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted --> <end value="[integer]"/><!-- 1..1 The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted --> <coordinateSystem><!-- 1..1 CodeableConcept The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based --></coordinateSystem> <reverseComplement value="[boolean]"/><!-- 0..1 A flag that indicates whether the extracted sequence should be reverse complemented --> </extracted> <repeated> <!-- 0..1 A Molecular Sequence that is represented as a repeated sequence motif --> <sequenceMotif><!-- 1..1 Reference(MolecularDefinition) The sequence that defines the repeated motif --></sequenceMotif> <copyCount value="[integer]"/><!-- 1..1 The number of repeats (copies) of the sequence motif --> </repeated> <concatenated> <!-- 0..1 A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences --> <sequenceElement> <!-- 1..* One element of a concatenated Molecular Sequence --> <sequence><!-- 1..1 Reference(MolecularDefinition) The Molecular Sequence corresponding to this element --></sequence> <ordinalIndex value="[integer]"/><!-- 1..1 The ordinal position of this sequence element within the concatenated Molecular Sequence --> </sequenceElement> </concatenated> <relative> <!-- 0..1 A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence --> <startingMolecule><!-- 1..1 Reference(MolecularDefinition) The Molecular Sequence that serves as the starting sequence, on which edits will be applied --></startingMolecule> <edit> <!-- 0..* An edit (change) made to a sequence --> <editOrder value="[integer]"/><!-- 0..1 The order of this edit, relative to other edits on the starting sequence --> <coordinateSystem><!-- 1..1 CodeableConcept The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based --></coordinateSystem> <start value="[integer]"/><!-- 1..1 The start coordinate of the interval that will be edited --> <end value="[integer]"/><!-- 1..1 The end coordinate of the interval that will be edited --> <replacementMolecule><!-- 1..1 Reference(MolecularDefinition) The sequence that defines the replacement sequence used in the edit operation --></replacementMolecule> <replacedMolecule><!-- 0..1 Reference(MolecularDefinition) The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit --></replacedMolecule> </edit> </relative> </representation> </MolecularDefinition>
JSON Template
{ "resourceType" : "MolecularDefinition", // from Resource: id, meta, implicitRules, and language // from DomainResource: text, contained, extension, and modifierExtension "identifier" : [{ Identifier }], // Unique ID for this particular resource "type" : "<code>", // aa | dna | rna "location" : [{ // Location of this molecule "sequenceLocation" : { // Location of this molecule in context of a sequence "sequenceContext" : { Reference(MolecularDefinition) }, // R! Reference sequence "coordinateInterval" : { // Coordinate Interval for this location "numberingSystem" : { CodeableConcept }, // Coordinate System // start[x]: Start. One of these 2: "startQuantity" : { Quantity }, "startRange" : { Range }, // end[x]: End. One of these 2: "endQuantity" : { Quantity }, "endRange" : { Range } }, "strand" : { CodeableConcept } // Forward or Reverse }, "cytobandLocation" : { // Location of this molecule in context of a cytoband "genomeAssembly" : { // R! Reference Genome "organism" : { CodeableConcept }, // Species of the organism "build" : { CodeableConcept }, // Build number "accession" : { CodeableConcept }, // Accession // description[x]: Genome assemble description. One of these 2: "descriptionMarkdown" : "<markdown>", "descriptionString" : "<string>" }, "cytobandInterval" : { // R! Cytoband Interval "chromosome" : { CodeableConcept }, // R! Chromosome "startCytoband" : { // Start // arm[x]: Arm. One of these 2: "armCode" : "<code>", "armString" : "<string>", // region[x]: Region. One of these 2: "regionCode" : "<code>", "regionString" : "<string>", // band[x]: Band. One of these 2: "bandCode" : "<code>", "bandString" : "<string>", // subBand[x]: Sub-band. One of these 2: "subBandCode" : "<code>", "subBandString" : "<string>" }, "endCytoband" : { // End // arm[x]: Arm. One of these 2: "armCode" : "<code>", "armString" : "<string>", // region[x]: Region. One of these 2: "regionCode" : "<code>", "regionString" : "<string>", // band[x]: Band. One of these 2: "bandCode" : "<code>", "bandString" : "<string>", // subBand[x]: SuBand. One of these 2: "subBandCode" : "<code>", "subBandString" : "<string>" } } }, "featureLocation" : [{ // Location in context of a feature "geneId" : [{ CodeableConcept }] // Gene Id }] }], "memberState" : [{ Reference(MolecularDefinition) }], // Member "representation" : [{ // Representation "focus" : { CodeableConcept }, // The focus of the representation "code" : [{ CodeableConcept }], // A code of the representation "literal" : { // A literal representation "encoding" : { CodeableConcept }, // The encoding used for the expression of the primary sequence "value" : "<string>" // R! The primary (linear) sequence, expressed as a literal string }, "resolvable" : { Attachment }, // A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself "extracted" : { // A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence "startingMolecule" : { Reference(MolecularDefinition) }, // R! The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted "start" : <integer>, // R! The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted "end" : <integer>, // R! The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted "coordinateSystem" : { CodeableConcept }, // R! The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based "reverseComplement" : <boolean> // A flag that indicates whether the extracted sequence should be reverse complemented }, "repeated" : { // A Molecular Sequence that is represented as a repeated sequence motif "sequenceMotif" : { Reference(MolecularDefinition) }, // R! The sequence that defines the repeated motif "copyCount" : <integer> // R! The number of repeats (copies) of the sequence motif }, "concatenated" : { // A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences "sequenceElement" : [{ // R! One element of a concatenated Molecular Sequence "sequence" : { Reference(MolecularDefinition) }, // R! The Molecular Sequence corresponding to this element "ordinalIndex" : <integer> // R! The ordinal position of this sequence element within the concatenated Molecular Sequence }] }, "relative" : { // A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence "startingMolecule" : { Reference(MolecularDefinition) }, // R! The Molecular Sequence that serves as the starting sequence, on which edits will be applied "edit" : [{ // An edit (change) made to a sequence "editOrder" : <integer>, // The order of this edit, relative to other edits on the starting sequence "coordinateSystem" : { CodeableConcept }, // R! The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based "start" : <integer>, // R! The start coordinate of the interval that will be edited "end" : <integer>, // R! The end coordinate of the interval that will be edited "replacementMolecule" : { Reference(MolecularDefinition) }, // R! The sequence that defines the replacement sequence used in the edit operation "replacedMolecule" : { Reference(MolecularDefinition) } // The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit }] } }] }
Turtle Template
@prefix fhir: <http://hl7.org/fhir/> . [ a fhir:MolecularDefinition; fhir:nodeRole fhir:treeRoot; # if this is the parser root # from Resource: .id, .meta, .implicitRules, and .language # from DomainResource: .text, .contained, .extension, and .modifierExtension fhir:identifier ( [ Identifier ] ... ) ; # 0..* Unique ID for this particular resource fhir:type [ code ] ; # 0..1 aa | dna | rna fhir:location ( [ # 0..* Location of this molecule fhir:sequenceLocation [ # 0..1 Location of this molecule in context of a sequence fhir:sequenceContext [ Reference(MolecularDefinition) ] ; # 1..1 Reference sequence fhir:coordinateInterval [ # 0..1 Coordinate Interval for this location fhir:numberingSystem [ CodeableConcept ] ; # 0..1 Coordinate System # start[x] : 0..1 Start. One of these 2 fhir:start [ a fhir:Quantity ; Quantity ] fhir:start [ a fhir:Range ; Range ] # end[x] : 0..1 End. One of these 2 fhir:end [ a fhir:Quantity ; Quantity ] fhir:end [ a fhir:Range ; Range ] ] ; fhir:strand [ CodeableConcept ] ; # 0..1 Forward or Reverse ] ; fhir:cytobandLocation [ # 0..1 Location of this molecule in context of a cytoband fhir:genomeAssembly [ # 1..1 Reference Genome fhir:organism [ CodeableConcept ] ; # 0..1 Species of the organism fhir:build [ CodeableConcept ] ; # 0..1 Build number fhir:accession [ CodeableConcept ] ; # 0..1 Accession # description[x] : 0..1 Genome assemble description. One of these 2 fhir:description [ a fhir:markdown ; markdown ] fhir:description [ a fhir:string ; string ] ] ; fhir:cytobandInterval [ # 1..1 Cytoband Interval fhir:chromosome [ CodeableConcept ] ; # 1..1 Chromosome fhir:startCytoband [ # 0..1 Start # arm[x] : 0..1 Arm. One of these 2 fhir:arm [ a fhir:code ; code ] fhir:arm [ a fhir:string ; string ] # region[x] : 0..1 Region. One of these 2 fhir:region [ a fhir:code ; code ] fhir:region [ a fhir:string ; string ] # band[x] : 0..1 Band. One of these 2 fhir:band [ a fhir:code ; code ] fhir:band [ a fhir:string ; string ] # subBand[x] : 0..1 Sub-band. One of these 2 fhir:subBand [ a fhir:code ; code ] fhir:subBand [ a fhir:string ; string ] ] ; fhir:endCytoband [ # 0..1 End # arm[x] : 0..1 Arm. One of these 2 fhir:arm [ a fhir:code ; code ] fhir:arm [ a fhir:string ; string ] # region[x] : 0..1 Region. One of these 2 fhir:region [ a fhir:code ; code ] fhir:region [ a fhir:string ; string ] # band[x] : 0..1 Band. One of these 2 fhir:band [ a fhir:code ; code ] fhir:band [ a fhir:string ; string ] # subBand[x] : 0..1 SuBand. One of these 2 fhir:subBand [ a fhir:code ; code ] fhir:subBand [ a fhir:string ; string ] ] ; ] ; ] ; fhir:featureLocation ( [ # 0..* Location in context of a feature fhir:geneId ( [ CodeableConcept ] ... ) ; # 0..* Gene Id ] ... ) ; ] ... ) ; fhir:memberState ( [ Reference(MolecularDefinition) ] ... ) ; # 0..* Member fhir:representation ( [ # 0..* Representation fhir:focus [ CodeableConcept ] ; # 0..1 The focus of the representation fhir:code ( [ CodeableConcept ] ... ) ; # 0..* A code of the representation fhir:literal [ # 0..1 A literal representation fhir:encoding [ CodeableConcept ] ; # 0..1 The encoding used for the expression of the primary sequence fhir:value [ string ] ; # 1..1 The primary (linear) sequence, expressed as a literal string ] ; fhir:resolvable [ Attachment ] ; # 0..1 A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself fhir:extracted [ # 0..1 A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence fhir:startingMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted fhir:start [ integer ] ; # 1..1 The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted fhir:end [ integer ] ; # 1..1 The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted fhir:coordinateSystem [ CodeableConcept ] ; # 1..1 The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based fhir:reverseComplement [ boolean ] ; # 0..1 A flag that indicates whether the extracted sequence should be reverse complemented ] ; fhir:repeated [ # 0..1 A Molecular Sequence that is represented as a repeated sequence motif fhir:sequenceMotif [ Reference(MolecularDefinition) ] ; # 1..1 The sequence that defines the repeated motif fhir:copyCount [ integer ] ; # 1..1 The number of repeats (copies) of the sequence motif ] ; fhir:concatenated [ # 0..1 A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences fhir:sequenceElement ( [ # 1..* One element of a concatenated Molecular Sequence fhir:sequence [ Reference(MolecularDefinition) ] ; # 1..1 The Molecular Sequence corresponding to this element fhir:ordinalIndex [ integer ] ; # 1..1 The ordinal position of this sequence element within the concatenated Molecular Sequence ] ... ) ; ] ; fhir:relative [ # 0..1 A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence fhir:startingMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The Molecular Sequence that serves as the starting sequence, on which edits will be applied fhir:edit ( [ # 0..* An edit (change) made to a sequence fhir:editOrder [ integer ] ; # 0..1 The order of this edit, relative to other edits on the starting sequence fhir:coordinateSystem [ CodeableConcept ] ; # 1..1 The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based fhir:start [ integer ] ; # 1..1 The start coordinate of the interval that will be edited fhir:end [ integer ] ; # 1..1 The end coordinate of the interval that will be edited fhir:replacementMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The sequence that defines the replacement sequence used in the edit operation fhir:replacedMolecule [ Reference(MolecularDefinition) ] ; # 0..1 The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit ] ... ) ; ] ; ] ... ) ; ]
Changes from both R4 and R4B
This resource did not exist in Release R4
See the Full Difference for further information
This analysis is available for R4 as XML or JSON and for R4B as XML or JSON.
Structure
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
MolecularDefinition | TU | DomainResource | Representation of a molecular definition Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension | |
identifier | Σ | 0..* | Identifier | Unique ID for this particular resource |
type | Σ | 0..1 | code | aa | dna | rna Binding: sequence Type (Required) |
location | Σ | 0..* | BackboneElement | Location of this molecule |
sequenceLocation | Σ | 0..1 | BackboneElement | Location of this molecule in context of a sequence |
sequenceContext | Σ | 1..1 | Reference(MolecularDefinition) | Reference sequence |
coordinateInterval | Σ | 0..1 | BackboneElement | Coordinate Interval for this location |
numberingSystem | Σ | 0..1 | CodeableConcept | Coordinate System |
start[x] | Σ | 0..1 | Start | |
startQuantity | Quantity | |||
startRange | Range | |||
end[x] | Σ | 0..1 | End | |
endQuantity | Quantity | |||
endRange | Range | |||
strand | 0..1 | CodeableConcept | Forward or Reverse | |
cytobandLocation | Σ | 0..1 | BackboneElement | Location of this molecule in context of a cytoband |
genomeAssembly | Σ | 1..1 | BackboneElement | Reference Genome |
organism | 0..1 | CodeableConcept | Species of the organism | |
build | 0..1 | CodeableConcept | Build number | |
accession | 0..1 | CodeableConcept | Accession | |
description[x] | 0..1 | Genome assemble description | ||
descriptionMarkdown | markdown | |||
descriptionString | string | |||
cytobandInterval | Σ | 1..1 | BackboneElement | Cytoband Interval |
chromosome | Σ | 1..1 | CodeableConcept | Chromosome |
startCytoband | Σ | 0..1 | BackboneElement | Start |
arm[x] | 0..1 | Arm | ||
armCode | code | |||
armString | string | |||
region[x] | 0..1 | Region | ||
regionCode | code | |||
regionString | string | |||
band[x] | 0..1 | Band | ||
bandCode | code | |||
bandString | string | |||
subBand[x] | 0..1 | Sub-band | ||
subBandCode | code | |||
subBandString | string | |||
endCytoband | Σ | 0..1 | BackboneElement | End |
arm[x] | 0..1 | Arm | ||
armCode | code | |||
armString | string | |||
region[x] | 0..1 | Region | ||
regionCode | code | |||
regionString | string | |||
band[x] | 0..1 | Band | ||
bandCode | code | |||
bandString | string | |||
subBand[x] | 0..1 | SuBand | ||
subBandCode | code | |||
subBandString | string | |||
featureLocation | Σ | 0..* | BackboneElement | Location in context of a feature |
geneId | Σ | 0..* | CodeableConcept | Gene Id |
memberState | Σ | 0..* | Reference(MolecularDefinition) | Member |
representation | Σ | 0..* | BackboneElement | Representation |
focus | Σ | 0..1 | CodeableConcept | The focus of the representation |
code | Σ | 0..* | CodeableConcept | A code of the representation |
literal | Σ | 0..1 | BackboneElement | A literal representation |
encoding | Σ | 0..1 | CodeableConcept | The encoding used for the expression of the primary sequence |
value | Σ | 1..1 | string | The primary (linear) sequence, expressed as a literal string |
resolvable | Σ | 0..1 | Attachment | A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself |
extracted | Σ | 0..1 | BackboneElement | A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence |
startingMolecule | Σ | 1..1 | Reference(MolecularDefinition) | The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted |
start | Σ | 1..1 | integer | The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted |
end | Σ | 1..1 | integer | The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted |
coordinateSystem | Σ | 1..1 | CodeableConcept | The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based |
reverseComplement | Σ | 0..1 | boolean | A flag that indicates whether the extracted sequence should be reverse complemented |
repeated | Σ | 0..1 | BackboneElement | A Molecular Sequence that is represented as a repeated sequence motif |
sequenceMotif | Σ | 1..1 | Reference(MolecularDefinition) | The sequence that defines the repeated motif |
copyCount | Σ | 1..1 | integer | The number of repeats (copies) of the sequence motif |
concatenated | Σ | 0..1 | BackboneElement | A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences |
sequenceElement | Σ | 1..* | BackboneElement | One element of a concatenated Molecular Sequence |
sequence | Σ | 1..1 | Reference(MolecularDefinition) | The Molecular Sequence corresponding to this element |
ordinalIndex | Σ | 1..1 | integer | The ordinal position of this sequence element within the concatenated Molecular Sequence |
relative | Σ | 0..1 | BackboneElement | A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence |
startingMolecule | Σ | 1..1 | Reference(MolecularDefinition) | The Molecular Sequence that serves as the starting sequence, on which edits will be applied |
edit | Σ | 0..* | BackboneElement | An edit (change) made to a sequence |
editOrder | 0..1 | integer | The order of this edit, relative to other edits on the starting sequence | |
coordinateSystem | Σ | 1..1 | CodeableConcept | The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based Binding: LL5323-2 (Extensible) |
start | Σ | 1..1 | integer | The start coordinate of the interval that will be edited |
end | Σ | 1..1 | integer | The end coordinate of the interval that will be edited |
replacementMolecule | Σ | 1..1 | Reference(MolecularDefinition) | The sequence that defines the replacement sequence used in the edit operation |
replacedMolecule | Σ | 0..1 | Reference(MolecularDefinition) | The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit |
Documentation for this format |
See the Extensions for this resource
XML Template
<MolecularDefinition xmlns="http://hl7.org/fhir"> <!-- from Resource: id, meta, implicitRules, and language --> <!-- from DomainResource: text, contained, extension, and modifierExtension --> <identifier><!-- 0..* Identifier Unique ID for this particular resource --></identifier> <type value="[code]"/><!-- 0..1 aa | dna | rna --> <location> <!-- 0..* Location of this molecule --> <sequenceLocation> <!-- 0..1 Location of this molecule in context of a sequence --> <sequenceContext><!-- 1..1 Reference(MolecularDefinition) Reference sequence --></sequenceContext> <coordinateInterval> <!-- 0..1 Coordinate Interval for this location --> <numberingSystem><!-- 0..1 CodeableConcept Coordinate System --></numberingSystem> <start[x]><!-- 0..1 Quantity|Range Start --></start[x]> <end[x]><!-- 0..1 Quantity|Range End --></end[x]> </coordinateInterval> <strand><!-- 0..1 CodeableConcept Forward or Reverse --></strand> </sequenceLocation> <cytobandLocation> <!-- 0..1 Location of this molecule in context of a cytoband --> <genomeAssembly> <!-- 1..1 Reference Genome --> <organism><!-- 0..1 CodeableConcept Species of the organism --></organism> <build><!-- 0..1 CodeableConcept Build number --></build> <accession><!-- 0..1 CodeableConcept Accession --></accession> <description[x]><!-- 0..1 markdown|string Genome assemble description --></description[x]> </genomeAssembly> <cytobandInterval> <!-- 1..1 Cytoband Interval --> <chromosome><!-- 1..1 CodeableConcept Chromosome --></chromosome> <startCytoband> <!-- 0..1 Start --> <arm[x]><!-- 0..1 code|string Arm --></arm[x]> <region[x]><!-- 0..1 code|string Region --></region[x]> <band[x]><!-- 0..1 code|string Band --></band[x]> <subBand[x]><!-- 0..1 code|string Sub-band --></subBand[x]> </startCytoband> <endCytoband> <!-- 0..1 End --> <arm[x]><!-- 0..1 code|string Arm --></arm[x]> <region[x]><!-- 0..1 code|string Region --></region[x]> <band[x]><!-- 0..1 code|string Band --></band[x]> <subBand[x]><!-- 0..1 code|string SuBand --></subBand[x]> </endCytoband> </cytobandInterval> </cytobandLocation> <featureLocation> <!-- 0..* Location in context of a feature --> <geneId><!-- 0..* CodeableConcept Gene Id --></geneId> </featureLocation> </location> <memberState><!-- 0..* Reference(MolecularDefinition) Member --></memberState> <representation> <!-- 0..* Representation --> <focus><!-- 0..1 CodeableConcept The focus of the representation --></focus> <code><!-- 0..* CodeableConcept A code of the representation --></code> <literal> <!-- 0..1 A literal representation --> <encoding><!-- 0..1 CodeableConcept The encoding used for the expression of the primary sequence --></encoding> <value value="[string]"/><!-- 1..1 The primary (linear) sequence, expressed as a literal string --> </literal> <resolvable><!-- 0..1 Attachment A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself --></resolvable> <extracted> <!-- 0..1 A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence --> <startingMolecule><!-- 1..1 Reference(MolecularDefinition) The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted --></startingMolecule> <start value="[integer]"/><!-- 1..1 The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted --> <end value="[integer]"/><!-- 1..1 The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted --> <coordinateSystem><!-- 1..1 CodeableConcept The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based --></coordinateSystem> <reverseComplement value="[boolean]"/><!-- 0..1 A flag that indicates whether the extracted sequence should be reverse complemented --> </extracted> <repeated> <!-- 0..1 A Molecular Sequence that is represented as a repeated sequence motif --> <sequenceMotif><!-- 1..1 Reference(MolecularDefinition) The sequence that defines the repeated motif --></sequenceMotif> <copyCount value="[integer]"/><!-- 1..1 The number of repeats (copies) of the sequence motif --> </repeated> <concatenated> <!-- 0..1 A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences --> <sequenceElement> <!-- 1..* One element of a concatenated Molecular Sequence --> <sequence><!-- 1..1 Reference(MolecularDefinition) The Molecular Sequence corresponding to this element --></sequence> <ordinalIndex value="[integer]"/><!-- 1..1 The ordinal position of this sequence element within the concatenated Molecular Sequence --> </sequenceElement> </concatenated> <relative> <!-- 0..1 A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence --> <startingMolecule><!-- 1..1 Reference(MolecularDefinition) The Molecular Sequence that serves as the starting sequence, on which edits will be applied --></startingMolecule> <edit> <!-- 0..* An edit (change) made to a sequence --> <editOrder value="[integer]"/><!-- 0..1 The order of this edit, relative to other edits on the starting sequence --> <coordinateSystem><!-- 1..1 CodeableConcept The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based --></coordinateSystem> <start value="[integer]"/><!-- 1..1 The start coordinate of the interval that will be edited --> <end value="[integer]"/><!-- 1..1 The end coordinate of the interval that will be edited --> <replacementMolecule><!-- 1..1 Reference(MolecularDefinition) The sequence that defines the replacement sequence used in the edit operation --></replacementMolecule> <replacedMolecule><!-- 0..1 Reference(MolecularDefinition) The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit --></replacedMolecule> </edit> </relative> </representation> </MolecularDefinition>
JSON Template
{ "resourceType" : "MolecularDefinition", // from Resource: id, meta, implicitRules, and language // from DomainResource: text, contained, extension, and modifierExtension "identifier" : [{ Identifier }], // Unique ID for this particular resource "type" : "<code>", // aa | dna | rna "location" : [{ // Location of this molecule "sequenceLocation" : { // Location of this molecule in context of a sequence "sequenceContext" : { Reference(MolecularDefinition) }, // R! Reference sequence "coordinateInterval" : { // Coordinate Interval for this location "numberingSystem" : { CodeableConcept }, // Coordinate System // start[x]: Start. One of these 2: "startQuantity" : { Quantity }, "startRange" : { Range }, // end[x]: End. One of these 2: "endQuantity" : { Quantity }, "endRange" : { Range } }, "strand" : { CodeableConcept } // Forward or Reverse }, "cytobandLocation" : { // Location of this molecule in context of a cytoband "genomeAssembly" : { // R! Reference Genome "organism" : { CodeableConcept }, // Species of the organism "build" : { CodeableConcept }, // Build number "accession" : { CodeableConcept }, // Accession // description[x]: Genome assemble description. One of these 2: "descriptionMarkdown" : "<markdown>", "descriptionString" : "<string>" }, "cytobandInterval" : { // R! Cytoband Interval "chromosome" : { CodeableConcept }, // R! Chromosome "startCytoband" : { // Start // arm[x]: Arm. One of these 2: "armCode" : "<code>", "armString" : "<string>", // region[x]: Region. One of these 2: "regionCode" : "<code>", "regionString" : "<string>", // band[x]: Band. One of these 2: "bandCode" : "<code>", "bandString" : "<string>", // subBand[x]: Sub-band. One of these 2: "subBandCode" : "<code>", "subBandString" : "<string>" }, "endCytoband" : { // End // arm[x]: Arm. One of these 2: "armCode" : "<code>", "armString" : "<string>", // region[x]: Region. One of these 2: "regionCode" : "<code>", "regionString" : "<string>", // band[x]: Band. One of these 2: "bandCode" : "<code>", "bandString" : "<string>", // subBand[x]: SuBand. One of these 2: "subBandCode" : "<code>", "subBandString" : "<string>" } } }, "featureLocation" : [{ // Location in context of a feature "geneId" : [{ CodeableConcept }] // Gene Id }] }], "memberState" : [{ Reference(MolecularDefinition) }], // Member "representation" : [{ // Representation "focus" : { CodeableConcept }, // The focus of the representation "code" : [{ CodeableConcept }], // A code of the representation "literal" : { // A literal representation "encoding" : { CodeableConcept }, // The encoding used for the expression of the primary sequence "value" : "<string>" // R! The primary (linear) sequence, expressed as a literal string }, "resolvable" : { Attachment }, // A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself "extracted" : { // A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence "startingMolecule" : { Reference(MolecularDefinition) }, // R! The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted "start" : <integer>, // R! The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted "end" : <integer>, // R! The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted "coordinateSystem" : { CodeableConcept }, // R! The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based "reverseComplement" : <boolean> // A flag that indicates whether the extracted sequence should be reverse complemented }, "repeated" : { // A Molecular Sequence that is represented as a repeated sequence motif "sequenceMotif" : { Reference(MolecularDefinition) }, // R! The sequence that defines the repeated motif "copyCount" : <integer> // R! The number of repeats (copies) of the sequence motif }, "concatenated" : { // A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences "sequenceElement" : [{ // R! One element of a concatenated Molecular Sequence "sequence" : { Reference(MolecularDefinition) }, // R! The Molecular Sequence corresponding to this element "ordinalIndex" : <integer> // R! The ordinal position of this sequence element within the concatenated Molecular Sequence }] }, "relative" : { // A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence "startingMolecule" : { Reference(MolecularDefinition) }, // R! The Molecular Sequence that serves as the starting sequence, on which edits will be applied "edit" : [{ // An edit (change) made to a sequence "editOrder" : <integer>, // The order of this edit, relative to other edits on the starting sequence "coordinateSystem" : { CodeableConcept }, // R! The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based "start" : <integer>, // R! The start coordinate of the interval that will be edited "end" : <integer>, // R! The end coordinate of the interval that will be edited "replacementMolecule" : { Reference(MolecularDefinition) }, // R! The sequence that defines the replacement sequence used in the edit operation "replacedMolecule" : { Reference(MolecularDefinition) } // The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit }] } }] }
Turtle Template
@prefix fhir: <http://hl7.org/fhir/> . [ a fhir:MolecularDefinition; fhir:nodeRole fhir:treeRoot; # if this is the parser root # from Resource: .id, .meta, .implicitRules, and .language # from DomainResource: .text, .contained, .extension, and .modifierExtension fhir:identifier ( [ Identifier ] ... ) ; # 0..* Unique ID for this particular resource fhir:type [ code ] ; # 0..1 aa | dna | rna fhir:location ( [ # 0..* Location of this molecule fhir:sequenceLocation [ # 0..1 Location of this molecule in context of a sequence fhir:sequenceContext [ Reference(MolecularDefinition) ] ; # 1..1 Reference sequence fhir:coordinateInterval [ # 0..1 Coordinate Interval for this location fhir:numberingSystem [ CodeableConcept ] ; # 0..1 Coordinate System # start[x] : 0..1 Start. One of these 2 fhir:start [ a fhir:Quantity ; Quantity ] fhir:start [ a fhir:Range ; Range ] # end[x] : 0..1 End. One of these 2 fhir:end [ a fhir:Quantity ; Quantity ] fhir:end [ a fhir:Range ; Range ] ] ; fhir:strand [ CodeableConcept ] ; # 0..1 Forward or Reverse ] ; fhir:cytobandLocation [ # 0..1 Location of this molecule in context of a cytoband fhir:genomeAssembly [ # 1..1 Reference Genome fhir:organism [ CodeableConcept ] ; # 0..1 Species of the organism fhir:build [ CodeableConcept ] ; # 0..1 Build number fhir:accession [ CodeableConcept ] ; # 0..1 Accession # description[x] : 0..1 Genome assemble description. One of these 2 fhir:description [ a fhir:markdown ; markdown ] fhir:description [ a fhir:string ; string ] ] ; fhir:cytobandInterval [ # 1..1 Cytoband Interval fhir:chromosome [ CodeableConcept ] ; # 1..1 Chromosome fhir:startCytoband [ # 0..1 Start # arm[x] : 0..1 Arm. One of these 2 fhir:arm [ a fhir:code ; code ] fhir:arm [ a fhir:string ; string ] # region[x] : 0..1 Region. One of these 2 fhir:region [ a fhir:code ; code ] fhir:region [ a fhir:string ; string ] # band[x] : 0..1 Band. One of these 2 fhir:band [ a fhir:code ; code ] fhir:band [ a fhir:string ; string ] # subBand[x] : 0..1 Sub-band. One of these 2 fhir:subBand [ a fhir:code ; code ] fhir:subBand [ a fhir:string ; string ] ] ; fhir:endCytoband [ # 0..1 End # arm[x] : 0..1 Arm. One of these 2 fhir:arm [ a fhir:code ; code ] fhir:arm [ a fhir:string ; string ] # region[x] : 0..1 Region. One of these 2 fhir:region [ a fhir:code ; code ] fhir:region [ a fhir:string ; string ] # band[x] : 0..1 Band. One of these 2 fhir:band [ a fhir:code ; code ] fhir:band [ a fhir:string ; string ] # subBand[x] : 0..1 SuBand. One of these 2 fhir:subBand [ a fhir:code ; code ] fhir:subBand [ a fhir:string ; string ] ] ; ] ; ] ; fhir:featureLocation ( [ # 0..* Location in context of a feature fhir:geneId ( [ CodeableConcept ] ... ) ; # 0..* Gene Id ] ... ) ; ] ... ) ; fhir:memberState ( [ Reference(MolecularDefinition) ] ... ) ; # 0..* Member fhir:representation ( [ # 0..* Representation fhir:focus [ CodeableConcept ] ; # 0..1 The focus of the representation fhir:code ( [ CodeableConcept ] ... ) ; # 0..* A code of the representation fhir:literal [ # 0..1 A literal representation fhir:encoding [ CodeableConcept ] ; # 0..1 The encoding used for the expression of the primary sequence fhir:value [ string ] ; # 1..1 The primary (linear) sequence, expressed as a literal string ] ; fhir:resolvable [ Attachment ] ; # 0..1 A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself fhir:extracted [ # 0..1 A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence fhir:startingMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted fhir:start [ integer ] ; # 1..1 The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted fhir:end [ integer ] ; # 1..1 The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted fhir:coordinateSystem [ CodeableConcept ] ; # 1..1 The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based fhir:reverseComplement [ boolean ] ; # 0..1 A flag that indicates whether the extracted sequence should be reverse complemented ] ; fhir:repeated [ # 0..1 A Molecular Sequence that is represented as a repeated sequence motif fhir:sequenceMotif [ Reference(MolecularDefinition) ] ; # 1..1 The sequence that defines the repeated motif fhir:copyCount [ integer ] ; # 1..1 The number of repeats (copies) of the sequence motif ] ; fhir:concatenated [ # 0..1 A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences fhir:sequenceElement ( [ # 1..* One element of a concatenated Molecular Sequence fhir:sequence [ Reference(MolecularDefinition) ] ; # 1..1 The Molecular Sequence corresponding to this element fhir:ordinalIndex [ integer ] ; # 1..1 The ordinal position of this sequence element within the concatenated Molecular Sequence ] ... ) ; ] ; fhir:relative [ # 0..1 A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence fhir:startingMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The Molecular Sequence that serves as the starting sequence, on which edits will be applied fhir:edit ( [ # 0..* An edit (change) made to a sequence fhir:editOrder [ integer ] ; # 0..1 The order of this edit, relative to other edits on the starting sequence fhir:coordinateSystem [ CodeableConcept ] ; # 1..1 The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based fhir:start [ integer ] ; # 1..1 The start coordinate of the interval that will be edited fhir:end [ integer ] ; # 1..1 The end coordinate of the interval that will be edited fhir:replacementMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The sequence that defines the replacement sequence used in the edit operation fhir:replacedMolecule [ Reference(MolecularDefinition) ] ; # 0..1 The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit ] ... ) ; ] ; ] ... ) ; ]
Changes from both R4 and R4B
This resource did not exist in Release R4
See the Full Difference for further information
This analysis is available for R4 as XML or JSON and for R4B as XML or JSON.
Additional definitions: Master Definition XML + JSON, XML Schema/Schematron + JSON Schema, ShEx (for Turtle) + see the extensions, the spreadsheet version & the dependency analysis
Path | ValueSet | Type | Documentation |
---|---|---|---|
MolecularDefinition.type | SequenceType | Required | Type if a sequence -- DNA, RNA, or amino acid sequence. |
MolecularDefinition.representation.relative.edit.coordinateSystem | http://loinc.org/LL5323-2/ | Extensible |
This resource supports three patterns for representing a sequence of interest:
The MolecularSequence resource is designed to represent a single sequence in an instance. Each sequence might have multiple representations, but implementers SHALL ensure all representations are for the same sequence.
literal
: This string element can be used to hold the sequence as a string of characters.
formatted
: This Attachment is used to refer to the sequence as embedded file content or via a URL reference.
This method can be used to refer to sequence data from in an external source. If the sequence is referring to a GA4GH repository, the formatted.url
should refer to a GA4GH compliant endpoint that conforms to GA4GH data models.
relative
: This complex element is used for encoding sequence. When the information of starting sequence and edits are provided, the observed sequence will be derived. Here is a picture below:
relative.ordinalPosition
: Indicates the order in which the sequence should be considered when putting multiple relative
instances together.
relative.sequenceRange
: Indicates the nucleotide range in the composed sequence when multiple relative
instances are used together.
These attributes help to clarify what sequence is being represented with less computation/inference on the recipient side. Implementers SHOULD use sequenceRange
first to determine order as the most reliable. If sequenceRange
is not present then ordinalPosition
SHOULD be used. Finally, if both sequenceRange
and ordinalPosition
are absent, then the order of the relative
data elements SHOULD be used to calculate a composition. It is the responsibility of the data sender to ensure the message can be consistently understood. Additionally, gaps in sequenceRange
are considered intentional (i.e. the composed sequence contains a sequence of N's, the placeholder nucleotide, for the gap range).
relative.startingSequence
: There are four optional ways to represent a starting sequence in MolecularSequence resource:
relative.startingSequence.sequenceCodeableConcept
: Starting sequence id in public database;relative.startingSequence.sequenceString
: Starting sequence string; relative.startingSequence.sequenceReference
: Reference to starting sequence stored in another sequence entity; relative.startingSequence.genomeAssembly
, relative.startingSequence.chromosome
: The combination of genome assembly and chromosome.
The relative.startingSequence.windowStart
and relative.startingSequence.windowEnd
defines a range from the starting sequence that is used to define a subsequence used as the starting sequence.
When saving the sequence information, the nucleic acid will be numbered with order. Some representations use a 0-based system (e.g. GA4GH API, BAM files) while some use a 1-based system (e.g. VCF file format). The element coordinateSystem contains this information.
relative.coordinateSystem
binds to a LOINC answer list, please review those answers here as well as the detailed description found here .
There are many considerations concerning the directionality of DNA or RNA. Here we are using relative.startingSequence.orientation
and relative.startingSequence.strand
. Orientation represents the sense of the sequence, which has different meanings depending on the type
. Strand represents the sequence writing order. Watson strand refers to 5' to 3' top strand (5' -> 3'), whereas Crick strand refers to 5' to 3' bottom strand (3' <- 5').
Only two possible values can be made by strand, watson
and crick
. Since the directionality of the sequence string might be represented in different ways in different omics scenario, below are examples of how to map other expressions into its correlated value:
Watson | Crick |
---|---|
5′-to-3′ direction | 3′-to-5′ direction |
+1 | -1 |
Sense | Antisense |
Positive | Negative |
There are attributes where the sequence is represented as a string of characters.
relative.startingSequence.sequenceString
relative.edit.replacementSequence
relative.edit.replacedSequence
literal
The characters used in these string representations of a sequence should be constrained to the IUPAC codes found here https://www.bioinformatics.org/sms2/iupac.html .
Search parameters for this resource. See also the full list of search parameters for this resource, and check the Extensions registry for search parameters on extensions related to this resource. The common parameters also apply. See Searching for more information about searching in REST, messaging, and services.
Name | Type | Description | Expression | In Common |
identifier | token | The unique identity for a particular sequence | MolecularDefinition.identifier | |
type | token | Amino Acid Sequence/ DNA Sequence / RNA Sequence | MolecularDefinition.type |