FHIR IG analytics| Package | hl7.fhir.uv.xver-r4.r5 |
| Resource Type | StructureDefinition |
| Id | StructureDefinition-ext-R4-MolecularSequence.referenceSeq.json |
| FHIR Version | R5 |
| Source | http://hl7.org/fhir/uv/xver-r4.r5/0.0.1-snapshot-2/StructureDefinition-ext-R4-MolecularSequence.referenceSeq.html |
| URL | http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.referenceSeq |
| Version | 0.0.1-snapshot-2 |
| Status | active |
| Date | 2025-09-01T22:36:30.973873+10:00 |
| Name | Ext_R4_MolecularSequence_referenceSeq |
| Title | Cross-version Extension for R4.MolecularSequence.referenceSeq for use in FHIR R5 |
| Realm | uv |
| Authority | hl7 |
| Description | This cross-version extension represents MolecularSequence.referenceSeq from http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.0.1 for use in FHIR R5. |
| Type | Extension |
| Kind | complex-type |
No resources found
| ValueSet | |
| R4-orientation-type-for-R5 | Cross-version VS for R4.orientationType for use in FHIR R5 |
| R4-sequence-referenceSeq-for-R5 | Cross-version VS for R4.ENSEMBL for use in FHIR R5 |
| R4-strand-type-for-R5 | Cross-version VS for R4.strandType for use in FHIR R5 |
| chromosome-human | chromosome-human |
No extension usage examples found
Note: links and images are rebased to the (stated) source
Generated Narrative: StructureDefinition ext-R4-MolecularSequence.referenceSeq
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Extension | 0..1 | Extension(5.0.0) | A sequence used as reference | |
  Slices for extension | 0..* | Extension | Extension Slice: Unordered, Closed by value:url | |
   extension:chromosome | 0..1 | Extension | Chromosome containing genetic finding | |
  url | 1..1 | uri | "chromosome" | |
  value[x] | 0..1 | CodeableConcept | Chromosome containing genetic finding Binding: http://terminology.hl7.org/ValueSet/chromosome-human|0.2.0 (example): Chromosome number for human. | |
| extension:genomeBuild | 0..1 | Extension | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' | |
| url | 1..1 | uri | "genomeBuild" | |
 value[x] | 0..1 | string | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' | |
| extension:orientation | 0..1 | Extension | sense | antisense | |
| url | 1..1 | uri | "orientation" | |
| value[x] | 0..1 | code | sense | antisense Binding: R4_orientation_type_for_R5 (0.0.1-snapshot-2) (required): Type for orientation. | |
| extension:referenceSeqId | 0..1 | Extension | Reference identifier | |
| url | 1..1 | uri | "referenceSeqId" | |
| value[x] | 0..1 | CodeableConcept | Reference identifier Binding: R4_sequence_referenceSeq_for_R5 (0.0.1-snapshot-2) (example): Reference identifier. | |
| extension:referenceSeqPointer | 0..1 | Extension | A pointer to another MolecularSequence entity as reference sequence | |
| url | 1..1 | uri | "referenceSeqPointer" | |
 value[x] | 0..1 | Reference() | A pointer to another MolecularSequence entity as reference sequence | |
| extension:referenceSeqString | 0..1 | Extension | A string to represent reference sequence | |
| url | 1..1 | uri | "referenceSeqString" | |
| value[x] | 0..1 | string | A string to represent reference sequence | |
| extension:strand | 0..1 | Extension | watson | crick | |
| url | 1..1 | uri | "strand" | |
| value[x] | 0..1 | code | watson | crick Binding: R4_strand_type_for_R5 (0.0.1-snapshot-2) (required): Type for strand. | |
| extension:windowStart | 0..1 | Extension | Start position of the window on the reference sequence | |
| url | 1..1 | uri | "windowStart" | |
| value[x] | 0..1 | integer | Start position of the window on the reference sequence | |
 extension:windowEnd | 0..1 | Extension | End position of the window on the reference sequence | |
 url | 1..1 | uri | "windowEnd" | |
| value[x] | 0..1 | integer | End position of the window on the reference sequence | |
 url | 1..1 | uri | "http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.referenceSeq" | |
| Documentation for this format | ||||
FHIR
FHIRsmith{
"resourceType": "StructureDefinition",
"id": "ext-R4-MolecularSequence.referenceSeq",
"text": {
"status": "extensions",
"div": "<!-- snip (see above) -->"
},
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode": "fhir"
},
{
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{
"url": "packageId",
"valueId": "hl7.fhir.uv.xver-r4.r5"
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{
"url": "version",
"valueString": "0.0.1-snapshot-2"
}
],
"url": "http://hl7.org/fhir/StructureDefinition/package-source"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-type-characteristics",
"valueCode": "can-bind"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
"valueInteger": 0,
"_valueInteger": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
"valueCanonical": "http://hl7.org/fhir/4.0/ImplementationGuide/hl7.fhir.uv.xver-r4.r5"
}
]
}
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
"valueCode": "trial-use",
"_valueCode": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
"valueCanonical": "http://hl7.org/fhir/4.0/ImplementationGuide/hl7.fhir.uv.xver-r4.r5"
}
]
}
}
],
"url": "http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.referenceSeq",
"version": "0.0.1-snapshot-2",
"name": "Ext_R4_MolecularSequence_referenceSeq",
"title": "Cross-version Extension for R4.MolecularSequence.referenceSeq for use in FHIR R5",
"status": "active",
"experimental": false,
"date": "2025-09-01T22:36:30.973873+10:00",
"publisher": "FHIR Infrastructure",
"contact": [
{
"name": "FHIR Infrastructure",
"telecom": [
{
"system": "url",
"value": "http://www.hl7.org/Special/committees/fiwg"
}
]
}
],
"description": "This cross-version extension represents MolecularSequence.referenceSeq from http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.0.1 for use in FHIR R5.",
"jurisdiction": [
{
"coding": [
{
"system": "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code": "001",
"display": "World"
}
]
}
],
"fhirVersion": "5.0.0",
"mapping": [
{
"identity": "rim",
"uri": "http://hl7.org/v3",
"name": "RIM Mapping"
}
],
"kind": "complex-type",
"abstract": false,
"context": [
{
"type": "element",
"expression": "MolecularSequence"
}
],
"type": "Extension",
"baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"derivation": "constraint",
"snapshot": {
"extension": [
{
"url": "http://hl7.org/fhir/tools/StructureDefinition/snapshot-base-version",
"valueString": "5.0.0"
}
],
"element": [
{
"id": "Extension",
"path": "Extension",
"short": "A sequence used as reference",
"definition": "A sequence that is used as a reference to describe variants that are present in a sequence analyzed.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
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{
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"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false
},
{
"id": "Extension.id",
"path": "Extension.id",
"representation": [
"xmlAttr"
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"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
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"base": {
"path": "Element.id",
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{
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{
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"path": "Extension.extension",
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{
"type": "value",
"path": "url"
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"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "closed"
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"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
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"type": [
{
"code": "Extension"
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"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
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{
"key": "ext-1",
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"expression": "extension.exists() != value.exists()",
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}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:chromosome",
"path": "Extension.extension",
"sliceName": "chromosome",
"short": "Chromosome containing genetic finding",
"definition": "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
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{
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"key": "ext-1",
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],
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},
{
"id": "Extension.extension:chromosome.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
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"max": "1"
},
"type": [
{
"extension": [
{
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"valueUrl": "id"
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],
"code": "http://hl7.org/fhirpath/System.String"
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},
{
"id": "Extension.extension:chromosome.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
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"max": "*"
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"type": [
{
"code": "Extension"
}
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"constraint": [
{
"key": "ele-1",
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"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
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"key": "ext-1",
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"human": "Must have either extensions or value[x], not both",
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}
],
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"isSummary": false,
"mapping": [
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]
},
{
"id": "Extension.extension:chromosome.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "chromosome",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:chromosome.value[x]",
"path": "Extension.extension.value[x]",
"short": "Chromosome containing genetic finding",
"definition": "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"binding": {
"strength": "example",
"description": "Chromosome number for human.",
"valueSet": "http://terminology.hl7.org/ValueSet/chromosome-human|0.2.0"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:genomeBuild",
"path": "Extension.extension",
"sliceName": "genomeBuild",
"short": "The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'",
"definition": "The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
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"max": "*"
},
"type": [
{
"code": "Extension"
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],
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{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:genomeBuild.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:genomeBuild.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:genomeBuild.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "genomeBuild",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:genomeBuild.value[x]",
"path": "Extension.extension.value[x]",
"short": "The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'",
"definition": "The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:orientation",
"path": "Extension.extension",
"sliceName": "orientation",
"short": "sense | antisense",
"definition": "A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the \"sense\" strand, and the opposite complementary strand is the \"antisense\" strand.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:orientation.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:orientation.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:orientation.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "orientation",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:orientation.value[x]",
"path": "Extension.extension.value[x]",
"short": "sense | antisense",
"definition": "A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the \"sense\" strand, and the opposite complementary strand is the \"antisense\" strand.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"binding": {
"strength": "required",
"description": "Type for orientation.",
"valueSet": "http://hl7.org/fhir/4.0/ValueSet/R4-orientation-type-for-R5|0.0.1-snapshot-2"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:referenceSeqId",
"path": "Extension.extension",
"sliceName": "referenceSeqId",
"short": "Reference identifier",
"definition": "Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:referenceSeqId.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:referenceSeqId.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:referenceSeqId.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "referenceSeqId",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:referenceSeqId.value[x]",
"path": "Extension.extension.value[x]",
"short": "Reference identifier",
"definition": "Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"binding": {
"strength": "example",
"description": "Reference identifier.",
"valueSet": "http://hl7.org/fhir/4.0/ValueSet/R4-sequence-referenceSeq-for-R5|0.0.1-snapshot-2"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:referenceSeqPointer",
"path": "Extension.extension",
"sliceName": "referenceSeqPointer",
"short": "A pointer to another MolecularSequence entity as reference sequence",
"definition": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:referenceSeqPointer.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:referenceSeqPointer.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:referenceSeqPointer.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "referenceSeqPointer",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:referenceSeqPointer.value[x]",
"path": "Extension.extension.value[x]",
"short": "A pointer to another MolecularSequence entity as reference sequence",
"definition": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:referenceSeqString",
"path": "Extension.extension",
"sliceName": "referenceSeqString",
"short": "A string to represent reference sequence",
"definition": "A string like \"ACGT\".",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:referenceSeqString.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:referenceSeqString.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:referenceSeqString.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "referenceSeqString",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:referenceSeqString.value[x]",
"path": "Extension.extension.value[x]",
"short": "A string to represent reference sequence",
"definition": "A string like \"ACGT\".",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:strand",
"path": "Extension.extension",
"sliceName": "strand",
"short": "watson | crick",
"definition": "An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:strand.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:strand.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:strand.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "strand",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:strand.value[x]",
"path": "Extension.extension.value[x]",
"short": "watson | crick",
"definition": "An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"binding": {
"strength": "required",
"description": "Type for strand.",
"valueSet": "http://hl7.org/fhir/4.0/ValueSet/R4-strand-type-for-R5|0.0.1-snapshot-2"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:windowStart",
"path": "Extension.extension",
"sliceName": "windowStart",
"short": "Start position of the window on the reference sequence",
"definition": "Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:windowStart.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:windowStart.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:windowStart.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "windowStart",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:windowStart.value[x]",
"path": "Extension.extension.value[x]",
"short": "Start position of the window on the reference sequence",
"definition": "Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:windowEnd",
"path": "Extension.extension",
"sliceName": "windowEnd",
"short": "End position of the window on the reference sequence",
"definition": "End position of the window on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:windowEnd.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:windowEnd.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:windowEnd.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "windowEnd",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:windowEnd.value[x]",
"path": "Extension.extension.value[x]",
"short": "End position of the window on the reference sequence",
"definition": "End position of the window on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.url",
"path": "Extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.referenceSeq",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.value[x]",
"path": "Extension.value[x]",
"short": "Value of extension",
"definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R5/extensibility.html) for a list).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "base64Binary"
},
{
"code": "boolean"
},
{
"code": "canonical"
},
{
"code": "code"
},
{
"code": "date"
},
{
"code": "dateTime"
},
{
"code": "decimal"
},
{
"code": "id"
},
{
"code": "instant"
},
{
"code": "integer"
},
{
"code": "integer64"
},
{
"code": "markdown"
},
{
"code": "oid"
},
{
"code": "positiveInt"
},
{
"code": "string"
},
{
"code": "time"
},
{
"code": "unsignedInt"
},
{
"code": "uri"
},
{
"code": "url"
},
{
"code": "uuid"
},
{
"code": "Address"
},
{
"code": "Age"
},
{
"code": "Annotation"
},
{
"code": "Attachment"
},
{
"code": "CodeableConcept"
},
{
"code": "CodeableReference"
},
{
"code": "Coding"
},
{
"code": "ContactPoint"
},
{
"code": "Count"
},
{
"code": "Distance"
},
{
"code": "Duration"
},
{
"code": "HumanName"
},
{
"code": "Identifier"
},
{
"code": "Money"
},
{
"code": "Period"
},
{
"code": "Quantity"
},
{
"code": "Range"
},
{
"code": "Ratio"
},
{
"code": "RatioRange"
},
{
"code": "Reference"
},
{
"code": "SampledData"
},
{
"code": "Signature"
},
{
"code": "Timing"
},
{
"code": "ContactDetail"
},
{
"code": "DataRequirement"
},
{
"code": "Expression"
},
{
"code": "ParameterDefinition"
},
{
"code": "RelatedArtifact"
},
{
"code": "TriggerDefinition"
},
{
"code": "UsageContext"
},
{
"code": "Availability"
},
{
"code": "ExtendedContactDetail"
},
{
"code": "Dosage"
},
{
"code": "Meta"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
}
]
},
"differential": {
"element": [
{
"id": "Extension",
"path": "Extension",
"short": "A sequence used as reference",
"definition": "A sequence that is used as a reference to describe variants that are present in a sequence analyzed.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension",
"path": "Extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "closed"
},
"min": 0,
"max": "*",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:chromosome",
"path": "Extension.extension",
"sliceName": "chromosome",
"short": "Chromosome containing genetic finding",
"definition": "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:chromosome.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "chromosome"
},
{
"id": "Extension.extension:chromosome.value[x]",
"path": "Extension.extension.value[x]",
"short": "Chromosome containing genetic finding",
"definition": "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"binding": {
"strength": "example",
"description": "Chromosome number for human.",
"valueSet": "http://terminology.hl7.org/ValueSet/chromosome-human|0.2.0"
}
},
{
"id": "Extension.extension:genomeBuild",
"path": "Extension.extension",
"sliceName": "genomeBuild",
"short": "The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'",
"definition": "The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:genomeBuild.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "genomeBuild"
},
{
"id": "Extension.extension:genomeBuild.value[x]",
"path": "Extension.extension.value[x]",
"short": "The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'",
"definition": "The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
]
},
{
"id": "Extension.extension:orientation",
"path": "Extension.extension",
"sliceName": "orientation",
"short": "sense | antisense",
"definition": "A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the \"sense\" strand, and the opposite complementary strand is the \"antisense\" strand.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:orientation.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "orientation"
},
{
"id": "Extension.extension:orientation.value[x]",
"path": "Extension.extension.value[x]",
"short": "sense | antisense",
"definition": "A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the \"sense\" strand, and the opposite complementary strand is the \"antisense\" strand.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"binding": {
"strength": "required",
"description": "Type for orientation.",
"valueSet": "http://hl7.org/fhir/4.0/ValueSet/R4-orientation-type-for-R5|0.0.1-snapshot-2"
}
},
{
"id": "Extension.extension:referenceSeqId",
"path": "Extension.extension",
"sliceName": "referenceSeqId",
"short": "Reference identifier",
"definition": "Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:referenceSeqId.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "referenceSeqId"
},
{
"id": "Extension.extension:referenceSeqId.value[x]",
"path": "Extension.extension.value[x]",
"short": "Reference identifier",
"definition": "Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"binding": {
"strength": "example",
"description": "Reference identifier.",
"valueSet": "http://hl7.org/fhir/4.0/ValueSet/R4-sequence-referenceSeq-for-R5|0.0.1-snapshot-2"
}
},
{
"id": "Extension.extension:referenceSeqPointer",
"path": "Extension.extension",
"sliceName": "referenceSeqPointer",
"short": "A pointer to another MolecularSequence entity as reference sequence",
"definition": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:referenceSeqPointer.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "referenceSeqPointer"
},
{
"id": "Extension.extension:referenceSeqPointer.value[x]",
"path": "Extension.extension.value[x]",
"short": "A pointer to another MolecularSequence entity as reference sequence",
"definition": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference"
}
]
},
{
"id": "Extension.extension:referenceSeqString",
"path": "Extension.extension",
"sliceName": "referenceSeqString",
"short": "A string to represent reference sequence",
"definition": "A string like \"ACGT\".",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:referenceSeqString.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "referenceSeqString"
},
{
"id": "Extension.extension:referenceSeqString.value[x]",
"path": "Extension.extension.value[x]",
"short": "A string to represent reference sequence",
"definition": "A string like \"ACGT\".",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
]
},
{
"id": "Extension.extension:strand",
"path": "Extension.extension",
"sliceName": "strand",
"short": "watson | crick",
"definition": "An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:strand.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "strand"
},
{
"id": "Extension.extension:strand.value[x]",
"path": "Extension.extension.value[x]",
"short": "watson | crick",
"definition": "An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"binding": {
"strength": "required",
"description": "Type for strand.",
"valueSet": "http://hl7.org/fhir/4.0/ValueSet/R4-strand-type-for-R5|0.0.1-snapshot-2"
}
},
{
"id": "Extension.extension:windowStart",
"path": "Extension.extension",
"sliceName": "windowStart",
"short": "Start position of the window on the reference sequence",
"definition": "Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:windowStart.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "windowStart"
},
{
"id": "Extension.extension:windowStart.value[x]",
"path": "Extension.extension.value[x]",
"short": "Start position of the window on the reference sequence",
"definition": "Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
]
},
{
"id": "Extension.extension:windowEnd",
"path": "Extension.extension",
"sliceName": "windowEnd",
"short": "End position of the window on the reference sequence",
"definition": "End position of the window on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:windowEnd.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "windowEnd"
},
{
"id": "Extension.extension:windowEnd.value[x]",
"path": "Extension.extension.value[x]",
"short": "End position of the window on the reference sequence",
"definition": "End position of the window on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"comment": "`MolecularSequence.referenceSeq` has no related element in R5:MolecularSequence",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
]
},
{
"id": "Extension.url",
"path": "Extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.referenceSeq"
}
]
}
}