FHIR IG analytics| Package | hl7.fhir.uv.xver-r4b.r3 |
| Resource Type | StructureDefinition |
| Id | StructureDefinition-profile-MolecularSequence-for-Sequence.json |
| FHIR Version | R3 |
| Source | http://hl7.org/fhir/uv/xver-r4b.r3/0.1.0/StructureDefinition-profile-MolecularSequence-for-Sequence.html |
| URL | http://hl7.org/fhir/4.3/StructureDefinition/profile-MolecularSequence-for-Sequence |
| Version | 0.1.0 |
| Status | active |
| Date | 2026-03-17T16:04:25.0089528-05:00 |
| Name | Profile_R4B_MolecularSequence_R3_Sequence |
| Title | Cross-version Profile for R4B.MolecularSequence for use in FHIR STU3 |
| Realm | uv |
| Authority | hl7 |
| Description | This cross-version profile allows R4B MolecularSequence content to be represented via FHIR STU3 Sequence resources. |
| Type | Sequence |
| Kind | resource |
No resources found
| StructureDefinition | ||
| hl7.fhir.uv.xver-r4b.r3#0.1.0 | extension-MolecularSequence.identifier | R4B: identifier additional types |
| hl7.fhir.uv.xver-r4b.r3#0.1.0 | extension-MolecularSequence.meta | R4B: meta additional types |
| hl7.fhir.uv.xver-r4b.r3#0.1.0 | extension-MolecularSequence.quality.roc | R4B: Receiver Operator Characteristic (ROC) Curve (new) |
| hl7.fhir.uv.xver-r4b.r3#0.1.0 | extension-MolecularSequence.referenceSeq.orientation | R4B: sense | antisense (new) |
| hl7.fhir.uv.xver-r4b.r3#0.1.0 | extension-MolecularSequence.referenceSeq.strand | R4B: watson | crick additional types |
| hl7.fhir.uv.xver-r4b.r5#0.1.0 | extension-MolecularSequence.structureVariant | R4B: Structural variant (new) |
| hl7.fhir.uv.xver-r4b.r3#0.1.0 | extension-MolecularSequence.text | R4B: text additional types |
| hl7.fhir.uv.xver-r4b.r3#0.1.0 | extension-MolecularSequence.type | R4B: type |
Note: links and images are rebased to the (stated) source
Generated Narrative: StructureDefinition profile-MolecularSequence-for-Sequence
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Sequence | 0..* | Sequence | Information about a biological sequence | |
  meta | ||||
   Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
   extension:meta | 0..1 | Meta | R4B: meta additional types URL: http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.meta | |
| text | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:text | 0..1 | (Complex) | R4B: text additional types URL: http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.text | |
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:structureVariant | 0..* | (Complex) | R4B: Structural variant (new) URL: http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.structureVariant | |
| identifier | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:identifier | 0..* | Identifier | R4B: identifier additional types URL: http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.identifier | |
| type | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:type | 0..1 | code | R4B: type URL: http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.type Binding: sequenceType (required): Type if a sequence -- DNA, RNA, or amino acid sequence. | |
| patient | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:patient | 0..1 | ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] | R4B: patient additional types URL: http://hl7.org/fhir/StructureDefinition/alternate-reference | |
| specimen | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:specimen | 0..1 | ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] | R4B: specimen additional types URL: http://hl7.org/fhir/StructureDefinition/alternate-reference | |
| device | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:device | 0..1 | ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] | R4B: device additional types URL: http://hl7.org/fhir/StructureDefinition/alternate-reference | |
| performer | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:performer | 0..1 | ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] | R4B: performer additional types URL: http://hl7.org/fhir/StructureDefinition/alternate-reference | |
| referenceSeq | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:orientation | 0..1 | code | R4B: sense | antisense (new) URL: http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.referenceSeq.orientation Binding: R4BOrientationTypeForR3 (0.1.0) (required): Type for orientation | |
| referenceSeqPointer | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:referenceSeqPointer | 0..1 | ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] | R4B: A pointer to another MolecularSequence entity as reference sequence additional types URL: http://hl7.org/fhir/StructureDefinition/alternate-reference | |
| strand | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:strand | 0..1 | code | R4B: watson | crick additional types URL: http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.referenceSeq.strand Binding: R4BStrandTypeForR3 (0.1.0) (required): Type for strand | |
| variant | ||||
| variantPointer | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:variantPointer | 0..1 | ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] | R4B: variantPointer additional types URL: http://hl7.org/fhir/StructureDefinition/alternate-reference | |
| quality | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:roc | 0..1 | (Complex) | R4B: Receiver Operator Characteristic (ROC) Curve (new) URL: http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.quality.roc | |
| pointer | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:pointer | 0..* | ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] | R4B: pointer additional types URL: http://hl7.org/fhir/StructureDefinition/alternate-reference | |
| Documentation for this format | ||||
FHIR
FHIRsmith{
"resourceType": "StructureDefinition",
"id": "profile-MolecularSequence-for-Sequence",
"text": {
"status": "extensions",
"div": "<!-- snip (see above) -->"
},
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode": "fhir"
},
{
"extension": [
{
"url": "packageId",
"valueId": "hl7.fhir.uv.xver-r4b.r3"
},
{
"url": "version",
"valueString": "0.1.0"
}
],
"url": "http://hl7.org/fhir/StructureDefinition/package-source"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
"valueInteger": 0,
"_valueInteger": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
"valueUri": "http://hl7.org/fhir/uv/xver/ImplementationGuide/hl7.fhir.uv.xver-r4b.r3"
}
]
}
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
"valueCode": "trial-use",
"_valueCode": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
"valueUri": "http://hl7.org/fhir/uv/xver/ImplementationGuide/hl7.fhir.uv.xver-r4b.r3"
}
]
}
}
],
"url": "http://hl7.org/fhir/4.3/StructureDefinition/profile-MolecularSequence-for-Sequence",
"version": "0.1.0",
"name": "Profile_R4B_MolecularSequence_R3_Sequence",
"title": "Cross-version Profile for R4B.MolecularSequence for use in FHIR STU3",
"status": "active",
"experimental": false,
"date": "2026-03-17T16:04:25.0089528-05:00",
"publisher": "FHIR Infrastructure",
"contact": [
{
"name": "FHIR Infrastructure",
"telecom": [
{
"system": "url",
"value": "http://www.hl7.org/Special/committees/fiwg"
}
]
}
],
"description": "This cross-version profile allows R4B MolecularSequence content to be represented via FHIR STU3 Sequence resources.",
"jurisdiction": [
{
"coding": [
{
"system": "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code": "001",
"display": "World"
}
]
}
],
"fhirVersion": "3.0.2",
"mapping": [
{
"identity": "w5",
"uri": "http://hl7.org/fhir/w5",
"name": "W5 Mapping"
},
{
"identity": "rim",
"uri": "http://hl7.org/v3",
"name": "RIM Mapping"
}
],
"kind": "resource",
"abstract": false,
"type": "Sequence",
"baseDefinition": "http://hl7.org/fhir/StructureDefinition/Sequence",
"derivation": "constraint",
"snapshot": {
"element": [
{
"id": "Sequence",
"path": "Sequence",
"short": "Information about a biological sequence",
"definition": "Raw data describing a biological sequence.",
"min": 0,
"max": "*",
"base": {
"path": "Sequence",
"min": 0,
"max": "*"
},
"constraint": [
{
"key": "dom-2",
"severity": "error",
"human": "If the resource is contained in another resource, it SHALL NOT contain nested Resources",
"expression": "contained.contained.empty()",
"xpath": "not(parent::f:contained and f:contained)",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource"
},
{
"key": "dom-1",
"severity": "error",
"human": "If the resource is contained in another resource, it SHALL NOT contain any narrative",
"expression": "contained.text.empty()",
"xpath": "not(parent::f:contained and f:text)",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource"
},
{
"key": "dom-4",
"severity": "error",
"human": "If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated",
"expression": "contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()",
"xpath": "not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource"
},
{
"key": "dom-3",
"severity": "error",
"human": "If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource",
"expression": "contained.where(('#'+id in %resource.descendants().reference).not()).empty()",
"xpath": "not(exists(for $id in f:contained/*/@id return $id[not(ancestor::f:contained/parent::*/descendant::f:reference/@value=concat('#', $id))]))",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource"
},
{
"key": "seq-3",
"severity": "error",
"human": "Only 0 and 1 are valid for coordinateSystem",
"expression": "coordinateSystem = 1 or coordinateSystem = 0",
"xpath": "count(f:coordinateSystem[@value=0 and @value=1]) = 1",
"source": "http://hl7.org/fhir/StructureDefinition/Sequence"
}
],
"mapping": [
{
"identity": "rim",
"map": "Entity. Role, or Act"
},
{
"identity": "w5",
"map": "clinical.diagnostics"
}
]
},
{
"id": "Sequence.id",
"path": "Sequence.id",
"short": "Logical id of this artifact",
"definition": "The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.",
"comment": "The only time that a resource does not have an id is when it is being submitted to the server using a create operation.",
"min": 0,
"max": "1",
"base": {
"path": "Resource.id",
"min": 0,
"max": "1"
},
"type": [
{
"code": "id"
}
],
"isSummary": true
},
{
"id": "Sequence.meta",
"path": "Sequence.meta",
"short": "Metadata about the resource",
"definition": "The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content may not always be associated with version changes to the resource.",
"min": 0,
"max": "1",
"base": {
"path": "Resource.meta",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Meta"
}
],
"isSummary": true
},
{
"id": "Sequence.meta.id",
"path": "Sequence.meta.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.meta.extension",
"path": "Sequence.meta.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.meta.extension:meta",
"path": "Sequence.meta.extension",
"sliceName": "meta",
"short": "R4B: meta additional types",
"definition": "R4B: `MolecularSequence.meta` additional types (Meta) additional types from child elements (lastUpdated, profile, security, source, tag, versionId)",
"comment": "Element `MolecularSequence.meta` is mapped to FHIR STU3 element `Sequence.meta` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.meta` do not cover the following types: Meta.\nThe mappings for `MolecularSequence.meta` do not cover the following types based on type expansion: lastUpdated, profile, security, source, tag, versionId.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.meta|0.1.0"
}
]
},
{
"id": "Sequence.meta.versionId",
"path": "Sequence.meta.versionId",
"short": "Version specific identifier",
"definition": "The version specific identifier, as it appears in the version portion of the URL. This values changes when the resource is created, updated, or deleted.",
"comment": "The server assigns this value, and ignores what the client specifies, except in the case that the server is imposing version integrity on updates/deletes.",
"min": 0,
"max": "1",
"base": {
"path": "Meta.versionId",
"min": 0,
"max": "1"
},
"type": [
{
"code": "id"
}
],
"isSummary": true
},
{
"id": "Sequence.meta.lastUpdated",
"path": "Sequence.meta.lastUpdated",
"short": "When the resource version last changed",
"definition": "When the resource last changed - e.g. when the version changed.",
"comment": "This value is always populated except when the resource is first being created. The server / resource manager sets this value; what a client provides is irrelevant.",
"min": 0,
"max": "1",
"base": {
"path": "Meta.lastUpdated",
"min": 0,
"max": "1"
},
"type": [
{
"code": "instant"
}
],
"isSummary": true
},
{
"id": "Sequence.meta.profile",
"path": "Sequence.meta.profile",
"short": "Profiles this resource claims to conform to",
"definition": "A list of profiles (references to [StructureDefinition](http://hl7.org/fhir/STU3/structuredefinition.html#) resources) that this resource claims to conform to. The URL is a reference to [StructureDefinition.url](http://hl7.org/fhir/STU3/).",
"comment": "It is up to the server and/or other infrastructure of policy to determine whether/how these claims are verified and/or updated over time. The list of profile URLs is a set.",
"min": 0,
"max": "*",
"base": {
"path": "Meta.profile",
"min": 0,
"max": "*"
},
"type": [
{
"code": "uri"
}
],
"isSummary": true
},
{
"id": "Sequence.meta.security",
"path": "Sequence.meta.security",
"short": "Security Labels applied to this resource",
"definition": "Security labels applied to this resource. These tags connect specific resources to the overall security policy and infrastructure.",
"comment": "The security labels can be updated without changing the stated version of the resource The list of security labels is a set. Uniqueness is based the system/code, and version and display are ignored.",
"min": 0,
"max": "*",
"base": {
"path": "Meta.security",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Coding"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "SecurityLabels"
}
],
"strength": "extensible",
"description": "Security Labels from the Healthcare Privacy and Security Classification System.",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/security-labels|3.0.2"
}
}
},
{
"id": "Sequence.meta.tag",
"path": "Sequence.meta.tag",
"short": "Tags applied to this resource",
"definition": "Tags applied to this resource. Tags are intended to be used to identify and relate resources to process and workflow, and applications are not required to consider the tags when interpreting the meaning of a resource.",
"comment": "The tags can be updated without changing the stated version of the resource. The list of tags is a set. Uniqueness is based the system/code, and version and display are ignored.",
"min": 0,
"max": "*",
"base": {
"path": "Meta.tag",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Coding"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "Tags"
}
],
"strength": "example",
"description": "Codes that represent various types of tags, commonly workflow-related; e.g. \"Needs review by Dr. Jones\"",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/common-tags|3.0.2"
}
}
},
{
"id": "Sequence.implicitRules",
"path": "Sequence.implicitRules",
"short": "A set of rules under which this content was created",
"definition": "A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content.",
"comment": "Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. \n\nThis element is labelled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation.",
"min": 0,
"max": "1",
"base": {
"path": "Resource.implicitRules",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"isModifier": true,
"isSummary": true
},
{
"id": "Sequence.language",
"path": "Sequence.language",
"short": "Language of the resource content",
"definition": "The base language in which the resource is written.",
"comment": "Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).",
"min": 0,
"max": "1",
"base": {
"path": "Resource.language",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet",
"valueReference": {
"reference": "http://hl7.org/fhir/ValueSet/all-languages|3.0.2"
}
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "Language"
}
],
"strength": "extensible",
"description": "A human language.",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/languages|3.0.2"
}
}
},
{
"id": "Sequence.text",
"path": "Sequence.text",
"short": "Text summary of the resource, for human interpretation",
"definition": "A human-readable narrative that contains a summary of the resource, and may be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it \"clinically safe\" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.",
"comment": "Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a \"text blob\" or where text is additionally entered raw or narrated and encoded in formation is added later.",
"alias": [
"narrative",
"html",
"xhtml",
"display"
],
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.text",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Narrative"
}
],
"condition": [
"dom-1"
],
"mapping": [
{
"identity": "rim",
"map": "Act.text?"
}
]
},
{
"id": "Sequence.text.id",
"path": "Sequence.text.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.text.extension",
"path": "Sequence.text.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.text.extension:text",
"path": "Sequence.text.extension",
"sliceName": "text",
"short": "R4B: text additional types",
"definition": "R4B: `MolecularSequence.text` additional types (Narrative) additional types from child elements (div, status)",
"comment": "Element `MolecularSequence.text` is mapped to FHIR STU3 element `Sequence.text` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.text` do not cover the following types: Narrative.\nThe mappings for `MolecularSequence.text` do not cover the following types based on type expansion: div, status.\nContained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a \"text blob\" or where text is additionally entered raw or narrated and encoded information is added later.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.text|0.1.0"
}
]
},
{
"id": "Sequence.text.status",
"path": "Sequence.text.status",
"short": "generated | extensions | additional | empty",
"definition": "The status of the narrative - whether it's entirely generated (from just the defined data or the extensions too), or whether a human authored it and it may contain additional data.",
"min": 1,
"max": "1",
"base": {
"path": "Narrative.status",
"min": 1,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "NarrativeStatus"
}
],
"strength": "required",
"description": "The status of a resource narrative",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/narrative-status|3.0.2"
}
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.text.div",
"path": "Sequence.text.div",
"short": "Limited xhtml content",
"definition": "The actual narrative content, a stripped down version of XHTML.",
"comment": "The contents of the html element are an XHTML fragment containing only the basic html formatting elements described in chapters 7-11 and 15 of the HTML 4.0 standard, <a> elements (either name or href), images and internally contained stylesheets. The XHTML content may not contain a head, a body, external stylesheet references, scripts, forms, base/link/xlink, frames, iframes and objects.",
"min": 1,
"max": "1",
"base": {
"path": "Narrative.div",
"min": 1,
"max": "1"
},
"type": [
{
"code": "xhtml"
}
],
"constraint": [
{
"key": "txt-1",
"severity": "error",
"human": "The narrative SHALL contain only the basic html formatting elements and attributes described in chapters 7-11 (except section 4 of chapter 9) and 15 of the HTML 4.0 standard, <a> elements (either name or href), images and internally contained style attributes",
"expression": "htmlchecks()",
"xpath": "not(descendant-or-self::*[not(local-name(.)=('a', 'abbr', 'acronym', 'b', 'big', 'blockquote', 'br', 'caption', 'cite', 'code', 'col', 'colgroup', 'dd', 'dfn', 'div', 'dl', 'dt', 'em', 'h1', 'h2', 'h3', 'h4', 'h5', 'h6', 'hr', 'i', 'img', 'li', 'ol', 'p', 'pre', 'q', 'samp', 'small', 'span', 'strong', 'sub', 'sup', 'table', 'tbody', 'td', 'tfoot', 'th', 'thead', 'tr', 'tt', 'ul', 'var'))]) and not(descendant-or-self::*/@*[not(name(.)=('abbr', 'accesskey', 'align', 'alt', 'axis', 'bgcolor', 'border', 'cellhalign', 'cellpadding', 'cellspacing', 'cellvalign', 'char', 'charoff', 'charset', 'cite', 'class', 'colspan', 'compact', 'coords', 'dir', 'frame', 'headers', 'height', 'href', 'hreflang', 'hspace', 'id', 'lang', 'longdesc', 'name', 'nowrap', 'rel', 'rev', 'rowspan', 'rules', 'scope', 'shape', 'span', 'src', 'start', 'style', 'summary', 'tabindex', 'title', 'type', 'valign', 'value', 'vspace', 'width'))])",
"source": "http://hl7.org/fhir/StructureDefinition/Sequence"
},
{
"key": "txt-2",
"severity": "error",
"human": "The narrative SHALL have some non-whitespace content",
"expression": "htmlchecks()",
"xpath": "descendant::text()[normalize-space(.)!=''] or descendant::h:img[@src]",
"source": "http://hl7.org/fhir/StructureDefinition/Sequence"
}
],
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.contained",
"path": "Sequence.contained",
"short": "Contained, inline Resources",
"definition": "These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.",
"comment": "This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again.",
"alias": [
"inline resources",
"anonymous resources",
"contained resources"
],
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.contained",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Resource"
}
],
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.extension",
"path": "Sequence.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.extension:structureVariant",
"path": "Sequence.extension",
"sliceName": "structureVariant",
"short": "R4B: Structural variant (new)",
"definition": "R4B: `MolecularSequence.structureVariant` (new:BackboneElement)",
"comment": "Element `MolecularSequence.structureVariant` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.structureVariant` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.structureVariant|0.1.0"
}
],
"condition": [
"ele-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() | (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier": false
},
{
"id": "Sequence.modifierExtension",
"path": "Sequence.modifierExtension",
"short": "Extensions that cannot be ignored",
"definition": "May be used to represent additional information that is not part of the basic definition of the resource, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.",
"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": "DomainResource.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.identifier",
"path": "Sequence.identifier",
"short": "Unique ID for this particular sequence. This is a FHIR-defined id",
"definition": "A unique identifier for this particular sequence instance. This is a FHIR-defined id.",
"requirements": "Allows sequences to be distinguished and referenced.",
"min": 0,
"max": "*",
"base": {
"path": "Sequence.identifier",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Identifier"
}
],
"isSummary": true,
"mapping": [
{
"identity": "w5",
"map": "id"
}
]
},
{
"id": "Sequence.identifier.id",
"path": "Sequence.identifier.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.identifier.extension",
"path": "Sequence.identifier.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.identifier.extension:identifier",
"path": "Sequence.identifier.extension",
"sliceName": "identifier",
"short": "R4B: identifier additional types",
"definition": "R4B: `MolecularSequence.identifier` additional types (Identifier) additional types from child elements (assigner, period, system, type, use, value)",
"comment": "Element `MolecularSequence.identifier` is mapped to FHIR STU3 element `Sequence.identifier` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.identifier` do not cover the following types: Identifier.\nThe mappings for `MolecularSequence.identifier` do not cover the following types based on type expansion: assigner, period, system, type, use, value.",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.identifier|0.1.0"
}
]
},
{
"id": "Sequence.identifier.use",
"path": "Sequence.identifier.use",
"short": "usual | official | temp | secondary (If known)",
"definition": "The purpose of this identifier.",
"comment": "This is labeled as \"Is Modifier\" because applications should not mistake a temporary id for a permanent one. Applications can assume that an identifier is permanent unless it explicitly says that it is temporary.",
"requirements": "Allows the appropriate identifier for a particular context of use to be selected from among a set of identifiers.",
"min": 0,
"max": "1",
"base": {
"path": "Identifier.use",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"isModifier": true,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "IdentifierUse"
}
],
"strength": "required",
"description": "Identifies the purpose for this identifier, if known .",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/identifier-use|3.0.2"
}
},
"mapping": [
{
"identity": "v2",
"map": "N/A"
},
{
"identity": "rim",
"map": "Role.code or implied by context"
}
]
},
{
"id": "Sequence.identifier.type",
"path": "Sequence.identifier.type",
"short": "Description of identifier",
"definition": "A coded type for the identifier that can be used to determine which identifier to use for a specific purpose.",
"comment": "This element deals only with general categories of identifiers. It SHOULD not be used for codes that correspond 1..1 with the Identifier.system. Some identifiers may fall into multiple categories due to common usage. \n\nWhere the system is known, a type is unnecessary because the type is always part of the system definition. However systems often need to handle identifiers where the system is not known. There is not a 1:1 relationship between type and system, since many different systems have the same type.",
"requirements": "Allows users to make use of identifiers when the identifier system is not known.",
"min": 0,
"max": "1",
"base": {
"path": "Identifier.type",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "IdentifierType"
}
],
"strength": "extensible",
"description": "A coded type for an identifier that can be used to determine which identifier to use for a specific purpose.",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/identifier-type|3.0.2"
}
},
"mapping": [
{
"identity": "v2",
"map": "CX.5"
},
{
"identity": "rim",
"map": "Role.code or implied by context"
}
]
},
{
"id": "Sequence.identifier.system",
"path": "Sequence.identifier.system",
"short": "The namespace for the identifier value",
"definition": "Establishes the namespace for the value - that is, a URL that describes a set values that are unique.",
"requirements": "There are many sets of identifiers. To perform matching of two identifiers, we need to know what set we're dealing with. The system identifies a particular set of unique identifiers.",
"min": 0,
"max": "1",
"base": {
"path": "Identifier.system",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"example": [
{
"label": "General",
"valueUri": "http://www.acme.com/identifiers/patient"
}
],
"isSummary": true,
"mapping": [
{
"identity": "v2",
"map": "CX.4 / EI-2-4"
},
{
"identity": "rim",
"map": "II.root or Role.id.root"
},
{
"identity": "servd",
"map": "./IdentifierType"
}
]
},
{
"id": "Sequence.identifier.value",
"path": "Sequence.identifier.value",
"short": "The value that is unique",
"definition": "The portion of the identifier typically relevant to the user and which is unique within the context of the system.",
"comment": "If the value is a full URI, then the system SHALL be urn:ietf:rfc:3986. The value's primary purpose is computational mapping. As a result, it may be normalized for comparison purposes (e.g. removing non-significant whitespace, dashes, etc.) A value formatted for human display can be conveyed using the [Rendered Value extension](http://hl7.org/fhir/STU3/extension-rendered-value.html).",
"min": 0,
"max": "1",
"base": {
"path": "Identifier.value",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"example": [
{
"label": "General",
"valueString": "123456"
}
],
"isSummary": true,
"mapping": [
{
"identity": "v2",
"map": "CX.1 / EI.1"
},
{
"identity": "rim",
"map": "II.extension or II.root if system indicates OID or GUID (Or Role.id.extension or root)"
},
{
"identity": "servd",
"map": "./Value"
}
]
},
{
"id": "Sequence.identifier.period",
"path": "Sequence.identifier.period",
"short": "Time period when id is/was valid for use",
"definition": "Time period during which identifier is/was valid for use.",
"min": 0,
"max": "1",
"base": {
"path": "Identifier.period",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Period"
}
],
"isSummary": true,
"mapping": [
{
"identity": "v2",
"map": "CX.7 + CX.8"
},
{
"identity": "rim",
"map": "Role.effectiveTime or implied by context"
},
{
"identity": "servd",
"map": "./StartDate and ./EndDate"
}
]
},
{
"id": "Sequence.identifier.assigner",
"path": "Sequence.identifier.assigner",
"short": "Organization that issued id (may be just text)",
"definition": "Organization that issued/manages the identifier.",
"comment": "The Identifier.assigner may omit the .reference element and only contain a .display element reflecting the name or other textual information about the assigning organization.",
"min": 0,
"max": "1",
"base": {
"path": "Identifier.assigner",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": "http://hl7.org/fhir/StructureDefinition/Organization"
}
],
"isSummary": true,
"mapping": [
{
"identity": "v2",
"map": "CX.4 / (CX.4,CX.9,CX.10)"
},
{
"identity": "rim",
"map": "II.assigningAuthorityName but note that this is an improper use by the definition of the field. Also Role.scoper"
},
{
"identity": "servd",
"map": "./IdentifierIssuingAuthority"
}
]
},
{
"id": "Sequence.type",
"path": "Sequence.type",
"short": "aa | dna | rna",
"definition": "Amino Acid Sequence/ DNA Sequence / RNA Sequence.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.type",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "sequenceType"
}
],
"strength": "example",
"description": "Type if a sequence -- DNA, RNA, or amino acid sequence",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/sequence-type|3.0.2"
}
}
},
{
"id": "Sequence.type.id",
"path": "Sequence.type.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"definition": "unique id for the element within a resource (for internal references)",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
]
},
{
"id": "Sequence.type.extension",
"path": "Sequence.type.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.type.extension:type",
"path": "Sequence.type.extension",
"sliceName": "type",
"short": "R4B: type",
"definition": "R4B: `MolecularSequence.type`",
"comment": "Element `MolecularSequence.type` is mapped to FHIR STU3 element `Sequence.type` as `Equivalent`.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.type|0.1.0"
}
],
"condition": [
"ele-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() | (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier": false
},
{
"id": "Sequence.type.value",
"path": "Sequence.type.value",
"representation": [
"xmlAttr"
],
"short": "Primitive value for code",
"definition": "Primitive value for code",
"min": 0,
"max": "1",
"base": {
"path": "string.value",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-regex",
"valueString": "[^\\s]+([\\s]?[^\\s]+)*"
}
],
"_code": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-json-type",
"valueString": "string"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-type",
"valueString": "xsd:token"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-rdf-type",
"valueString": "xsd:token"
}
]
}
}
]
},
{
"id": "Sequence.coordinateSystem",
"path": "Sequence.coordinateSystem",
"short": "Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)",
"definition": "Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).",
"min": 1,
"max": "1",
"base": {
"path": "Sequence.coordinateSystem",
"min": 1,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.patient",
"path": "Sequence.patient",
"short": "Who and/or what this is about",
"definition": "The patient whose sequencing results are described by this resource.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.patient",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": "http://hl7.org/fhir/StructureDefinition/Patient"
}
],
"isSummary": true
},
{
"id": "Sequence.patient.id",
"path": "Sequence.patient.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.patient.extension",
"path": "Sequence.patient.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.patient.extension:patient",
"path": "Sequence.patient.extension",
"sliceName": "patient",
"short": "R4B: patient additional types",
"definition": "R4B: `MolecularSequence.patient` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.patient` is mapped to FHIR STU3 element `Sequence.patient` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.patient` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.patient` with unmapped reference targets: Patient.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
},
{
"id": "Sequence.patient.reference",
"path": "Sequence.patient.reference",
"short": "Literal reference, Relative, internal or absolute URL",
"definition": "A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.",
"comment": "Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure \"/[type]/[id]\" then it should be assumed that the reference is to a FHIR RESTful server.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.reference",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"condition": [
"ref-1"
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.patient.identifier",
"path": "Sequence.patient.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the other resource. This is used when there is no way to reference the other resource directly, either because the entity is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.",
"comment": "When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. \n\nWhen both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference\n\nApplications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "Sequence.patient.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "Sequence.patient.display",
"short": "Text alternative for the resource",
"definition": "Plain text narrative that identifies the resource in addition to the resource reference.",
"comment": "This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.display",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.specimen",
"path": "Sequence.specimen",
"short": "Specimen used for sequencing",
"definition": "Specimen used for sequencing.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.specimen",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": "http://hl7.org/fhir/StructureDefinition/Specimen"
}
],
"isSummary": true
},
{
"id": "Sequence.specimen.id",
"path": "Sequence.specimen.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.specimen.extension",
"path": "Sequence.specimen.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.specimen.extension:specimen",
"path": "Sequence.specimen.extension",
"sliceName": "specimen",
"short": "R4B: specimen additional types",
"definition": "R4B: `MolecularSequence.specimen` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.specimen` is mapped to FHIR STU3 element `Sequence.specimen` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.specimen` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.specimen` with unmapped reference targets: Specimen.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
},
{
"id": "Sequence.specimen.reference",
"path": "Sequence.specimen.reference",
"short": "Literal reference, Relative, internal or absolute URL",
"definition": "A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.",
"comment": "Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure \"/[type]/[id]\" then it should be assumed that the reference is to a FHIR RESTful server.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.reference",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"condition": [
"ref-1"
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.specimen.identifier",
"path": "Sequence.specimen.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the other resource. This is used when there is no way to reference the other resource directly, either because the entity is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.",
"comment": "When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. \n\nWhen both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference\n\nApplications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "Sequence.specimen.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "Sequence.specimen.display",
"short": "Text alternative for the resource",
"definition": "Plain text narrative that identifies the resource in addition to the resource reference.",
"comment": "This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.display",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.device",
"path": "Sequence.device",
"short": "The method for sequencing",
"definition": "The method for sequencing, for example, chip information.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.device",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": "http://hl7.org/fhir/StructureDefinition/Device"
}
],
"isSummary": true
},
{
"id": "Sequence.device.id",
"path": "Sequence.device.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.device.extension",
"path": "Sequence.device.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.device.extension:device",
"path": "Sequence.device.extension",
"sliceName": "device",
"short": "R4B: device additional types",
"definition": "R4B: `MolecularSequence.device` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.device` is mapped to FHIR STU3 element `Sequence.device` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.device` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.device` with unmapped reference targets: Device.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
},
{
"id": "Sequence.device.reference",
"path": "Sequence.device.reference",
"short": "Literal reference, Relative, internal or absolute URL",
"definition": "A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.",
"comment": "Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure \"/[type]/[id]\" then it should be assumed that the reference is to a FHIR RESTful server.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.reference",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"condition": [
"ref-1"
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.device.identifier",
"path": "Sequence.device.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the other resource. This is used when there is no way to reference the other resource directly, either because the entity is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.",
"comment": "When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. \n\nWhen both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference\n\nApplications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "Sequence.device.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "Sequence.device.display",
"short": "Text alternative for the resource",
"definition": "Plain text narrative that identifies the resource in addition to the resource reference.",
"comment": "This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.display",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.performer",
"path": "Sequence.performer",
"short": "Who should be responsible for test result",
"definition": "The organization or lab that should be responsible for this result.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.performer",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": "http://hl7.org/fhir/StructureDefinition/Organization"
}
],
"isSummary": true
},
{
"id": "Sequence.performer.id",
"path": "Sequence.performer.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.performer.extension",
"path": "Sequence.performer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.performer.extension:performer",
"path": "Sequence.performer.extension",
"sliceName": "performer",
"short": "R4B: performer additional types",
"definition": "R4B: `MolecularSequence.performer` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.performer` is mapped to FHIR STU3 element `Sequence.performer` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.performer` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.performer` with unmapped reference targets: Organization.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
},
{
"id": "Sequence.performer.reference",
"path": "Sequence.performer.reference",
"short": "Literal reference, Relative, internal or absolute URL",
"definition": "A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.",
"comment": "Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure \"/[type]/[id]\" then it should be assumed that the reference is to a FHIR RESTful server.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.reference",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"condition": [
"ref-1"
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.performer.identifier",
"path": "Sequence.performer.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the other resource. This is used when there is no way to reference the other resource directly, either because the entity is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.",
"comment": "When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. \n\nWhen both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference\n\nApplications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "Sequence.performer.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "Sequence.performer.display",
"short": "Text alternative for the resource",
"definition": "Plain text narrative that identifies the resource in addition to the resource reference.",
"comment": "This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.display",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.quantity",
"path": "Sequence.quantity",
"short": "The number of copies of the seqeunce of interest. (RNASeq)",
"definition": "The number of copies of the seqeunce of interest. (RNASeq).",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quantity",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Quantity"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq",
"path": "Sequence.referenceSeq",
"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.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.referenceSeq",
"min": 0,
"max": "1"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() | (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key": "seq-4",
"severity": "error",
"human": "Only +1 and -1 are valid for strand",
"expression": "strand.empty() or strand = 1 or strand = -1",
"xpath": "not(exists(f:strand)) or count(f:strand[@value=-1 and @value=1]) = 1",
"source": "http://hl7.org/fhir/StructureDefinition/Sequence"
},
{
"key": "seq-5",
"severity": "error",
"human": "GenomeBuild and chromosome must be both contained if either one of them is contained",
"expression": "(chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())",
"xpath": "(exists(f:chromosome) and exists(f:genomeBuild)) or (not(exists(f:chromosome)) and not(exists(f:genomeBuild)))",
"source": "http://hl7.org/fhir/StructureDefinition/Sequence"
},
{
"key": "seq-6",
"severity": "error",
"human": "Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;",
"expression": "(genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1",
"xpath": "count(f:genomeBuild)+count(f:referenceSeqId)+count(f:referenceSeqPointer)+count(f:referenceSeqString)=1",
"source": "http://hl7.org/fhir/StructureDefinition/Sequence"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.id",
"path": "Sequence.referenceSeq.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.referenceSeq.extension",
"path": "Sequence.referenceSeq.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.referenceSeq.extension:orientation",
"path": "Sequence.referenceSeq.extension",
"sliceName": "orientation",
"short": "R4B: sense | antisense (new)",
"definition": "R4B: `MolecularSequence.referenceSeq.orientation` (new:code)",
"comment": "Element `MolecularSequence.referenceSeq.orientation` has a context of Sequence.referenceSeq based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.referenceSeq.orientation` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.referenceSeq.orientation|0.1.0"
}
],
"condition": [
"ele-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() | (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier": false
},
{
"id": "Sequence.referenceSeq.modifierExtension",
"path": "Sequence.referenceSeq.modifierExtension",
"short": "Extensions that cannot be ignored",
"definition": "May be used to represent additional information that is not part of the basic definition of the element, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.",
"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",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.referenceSeq.chromosome",
"path": "Sequence.referenceSeq.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)).",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.referenceSeq.chromosome",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "chromosome-human"
}
],
"strength": "example",
"description": "Chromosome number for human",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/chromosome-human|3.0.2"
}
}
},
{
"id": "Sequence.referenceSeq.genomeBuild",
"path": "Sequence.referenceSeq.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.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.referenceSeq.genomeBuild",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.referenceSeqId",
"path": "Sequence.referenceSeq.referenceSeqId",
"short": "Reference identifier",
"definition": "Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.referenceSeq.referenceSeqId",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "sequenceReference"
}
],
"strength": "example",
"description": "Reference identifier",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/sequence-referenceSeq|3.0.2"
}
}
},
{
"id": "Sequence.referenceSeq.referenceSeqPointer",
"path": "Sequence.referenceSeq.referenceSeqPointer",
"short": "A Pointer to another Sequence entity as reference sequence",
"definition": "A Pointer to another Sequence entity as reference sequence.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.referenceSeq.referenceSeqPointer",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": "http://hl7.org/fhir/StructureDefinition/Sequence"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.referenceSeqPointer.id",
"path": "Sequence.referenceSeq.referenceSeqPointer.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.referenceSeq.referenceSeqPointer.extension",
"path": "Sequence.referenceSeq.referenceSeqPointer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.referenceSeq.referenceSeqPointer.extension:referenceSeqPointer",
"path": "Sequence.referenceSeq.referenceSeqPointer.extension",
"sliceName": "referenceSeqPointer",
"short": "R4B: A pointer to another MolecularSequence entity as reference sequence additional types",
"definition": "R4B: `MolecularSequence.referenceSeq.referenceSeqPointer` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.referenceSeq.referenceSeqPointer` is mapped to FHIR STU3 element `Sequence.referenceSeq.referenceSeqPointer` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.referenceSeq.referenceSeqPointer` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.referenceSeq.referenceSeqPointer` with unmapped reference targets: MolecularSequence.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
},
{
"id": "Sequence.referenceSeq.referenceSeqPointer.reference",
"path": "Sequence.referenceSeq.referenceSeqPointer.reference",
"short": "Literal reference, Relative, internal or absolute URL",
"definition": "A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.",
"comment": "Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure \"/[type]/[id]\" then it should be assumed that the reference is to a FHIR RESTful server.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.reference",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"condition": [
"ref-1"
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.referenceSeq.referenceSeqPointer.identifier",
"path": "Sequence.referenceSeq.referenceSeqPointer.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the other resource. This is used when there is no way to reference the other resource directly, either because the entity is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.",
"comment": "When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. \n\nWhen both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference\n\nApplications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "Sequence.referenceSeq.referenceSeqPointer.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "Sequence.referenceSeq.referenceSeqPointer.display",
"short": "Text alternative for the resource",
"definition": "Plain text narrative that identifies the resource in addition to the resource reference.",
"comment": "This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.display",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.referenceSeq.referenceSeqString",
"path": "Sequence.referenceSeq.referenceSeqString",
"short": "A string to represent reference sequence",
"definition": "A string like \"ACGT\".",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.referenceSeq.referenceSeqString",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.strand",
"path": "Sequence.referenceSeq.strand",
"short": "Directionality of DNA ( +1/-1)",
"definition": "Directionality of DNA sequence. Available values are \"1\" for the plus strand (5' to 3')/Watson/Sense/positive and \"-1\" for the minus strand(3' to 5')/Crick/Antisense/negative.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.referenceSeq.strand",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.strand.id",
"path": "Sequence.referenceSeq.strand.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"definition": "unique id for the element within a resource (for internal references)",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
]
},
{
"id": "Sequence.referenceSeq.strand.extension",
"path": "Sequence.referenceSeq.strand.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.referenceSeq.strand.extension:strand",
"path": "Sequence.referenceSeq.strand.extension",
"sliceName": "strand",
"short": "R4B: watson | crick additional types",
"definition": "R4B: `MolecularSequence.referenceSeq.strand` additional types (code) additional types from child elements (value)",
"comment": "Element `MolecularSequence.referenceSeq.strand` is mapped to FHIR STU3 element `Sequence.referenceSeq.strand` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.referenceSeq.strand` do not cover the following types: code.\nThe mappings for `MolecularSequence.referenceSeq.strand` do not cover the following types based on type expansion: value.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.referenceSeq.strand|0.1.0"
}
],
"condition": [
"ele-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() | (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier": false
},
{
"id": "Sequence.referenceSeq.strand.value",
"path": "Sequence.referenceSeq.strand.value",
"representation": [
"xmlAttr"
],
"short": "Primitive value for integer",
"definition": "The actual value",
"min": 0,
"max": "1",
"base": {
"path": "integer.value",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-regex",
"valueString": "-?([0]|([1-9][0-9]*))"
}
],
"_code": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-json-type",
"valueString": "number"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-type",
"valueString": "xsd:int"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-rdf-type",
"valueString": "xsd:int"
}
]
}
}
],
"minValueInteger": -2147483648,
"maxValueInteger": 2147483647
},
{
"id": "Sequence.referenceSeq.windowStart",
"path": "Sequence.referenceSeq.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.",
"min": 1,
"max": "1",
"base": {
"path": "Sequence.referenceSeq.windowStart",
"min": 1,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.referenceSeq.windowEnd",
"path": "Sequence.referenceSeq.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 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.",
"min": 1,
"max": "1",
"base": {
"path": "Sequence.referenceSeq.windowEnd",
"min": 1,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.variant",
"path": "Sequence.variant",
"short": "Variant in sequence",
"definition": "The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.",
"min": 0,
"max": "*",
"base": {
"path": "Sequence.variant",
"min": 0,
"max": "*"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() | (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.id",
"path": "Sequence.variant.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.variant.extension",
"path": "Sequence.variant.extension",
"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. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to 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"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.variant.modifierExtension",
"path": "Sequence.variant.modifierExtension",
"short": "Extensions that cannot be ignored",
"definition": "May be used to represent additional information that is not part of the basic definition of the element, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.",
"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",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.variant.start",
"path": "Sequence.variant.start",
"short": "Start position of the variant on the reference sequence",
"definition": "Start position of the variant on the reference sequence.If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.variant.start",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.end",
"path": "Sequence.variant.end",
"short": "End position of the variant on the reference sequence",
"definition": "End position of the variant on the reference sequence.If the coordinate system is 0-based then end is 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.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.variant.end",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.observedAllele",
"path": "Sequence.variant.observedAllele",
"short": "Allele that was observed",
"definition": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.variant.observedAllele",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.referenceAllele",
"path": "Sequence.variant.referenceAllele",
"short": "Allele in the reference sequence",
"definition": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.variant.referenceAllele",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.cigar",
"path": "Sequence.variant.cigar",
"short": "Extended CIGAR string for aligning the sequence with reference bases",
"definition": "Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.variant.cigar",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.variantPointer",
"path": "Sequence.variant.variantPointer",
"short": "Pointer to observed variant information",
"definition": "A pointer to an Observation containing variant information.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.variant.variantPointer",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": "http://hl7.org/fhir/StructureDefinition/Observation"
}
],
"isSummary": true
},
{
"id": "Sequence.variant.variantPointer.id",
"path": "Sequence.variant.variantPointer.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.variant.variantPointer.extension",
"path": "Sequence.variant.variantPointer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.variant.variantPointer.extension:variantPointer",
"path": "Sequence.variant.variantPointer.extension",
"sliceName": "variantPointer",
"short": "R4B: variantPointer additional types",
"definition": "R4B: `MolecularSequence.variant.variantPointer` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.variant.variantPointer` is mapped to FHIR STU3 element `Sequence.variant.variantPointer` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.variant.variantPointer` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.variant.variantPointer` with unmapped reference targets: Observation.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
},
{
"id": "Sequence.variant.variantPointer.reference",
"path": "Sequence.variant.variantPointer.reference",
"short": "Literal reference, Relative, internal or absolute URL",
"definition": "A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.",
"comment": "Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure \"/[type]/[id]\" then it should be assumed that the reference is to a FHIR RESTful server.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.reference",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"condition": [
"ref-1"
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.variant.variantPointer.identifier",
"path": "Sequence.variant.variantPointer.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the other resource. This is used when there is no way to reference the other resource directly, either because the entity is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.",
"comment": "When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. \n\nWhen both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference\n\nApplications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "Sequence.variant.variantPointer.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "Sequence.variant.variantPointer.display",
"short": "Text alternative for the resource",
"definition": "Plain text narrative that identifies the resource in addition to the resource reference.",
"comment": "This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.display",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.observedSeq",
"path": "Sequence.observedSeq",
"short": "Sequence that was observed",
"definition": "Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.observedSeq",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.quality",
"path": "Sequence.quality",
"short": "An set of value as quality of sequence",
"definition": "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).",
"min": 0,
"max": "*",
"base": {
"path": "Sequence.quality",
"min": 0,
"max": "*"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() | (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.id",
"path": "Sequence.quality.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.quality.extension",
"path": "Sequence.quality.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.quality.extension:roc",
"path": "Sequence.quality.extension",
"sliceName": "roc",
"short": "R4B: Receiver Operator Characteristic (ROC) Curve (new)",
"definition": "R4B: `MolecularSequence.quality.roc` (new:BackboneElement)",
"comment": "Element `MolecularSequence.quality.roc` has a context of Sequence.quality based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.quality.roc` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.quality.roc|0.1.0"
}
],
"condition": [
"ele-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() | (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier": false
},
{
"id": "Sequence.quality.modifierExtension",
"path": "Sequence.quality.modifierExtension",
"short": "Extensions that cannot be ignored",
"definition": "May be used to represent additional information that is not part of the basic definition of the element, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.",
"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",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.quality.type",
"path": "Sequence.quality.type",
"short": "indel | snp | unknown",
"definition": "INDEL / SNP / Undefined variant.",
"min": 1,
"max": "1",
"base": {
"path": "Sequence.quality.type",
"min": 1,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "qualityType"
}
],
"strength": "required",
"description": "Type for quality report",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/quality-type|3.0.2"
}
}
},
{
"id": "Sequence.quality.standardSequence",
"path": "Sequence.quality.standardSequence",
"short": "Standard sequence for comparison",
"definition": "Gold standard sequence used for comparing against.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quality.standardSequence",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "qualityStandardSequence"
}
],
"strength": "example",
"description": "Reference identifier of the sequence that used to mark the quality of tested samples.",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence|3.0.2"
}
}
},
{
"id": "Sequence.quality.start",
"path": "Sequence.quality.start",
"short": "Start position of the sequence",
"definition": "Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quality.start",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.end",
"path": "Sequence.quality.end",
"short": "End position of the sequence",
"definition": "End position of the sequence.If the coordinate system is 0-based then end is 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.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quality.end",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.score",
"path": "Sequence.quality.score",
"short": "Quality score for the comparison",
"definition": "The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quality.score",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Quantity"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.method",
"path": "Sequence.quality.method",
"short": "Method to get quality",
"definition": "Which method is used to get sequence quality.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quality.method",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "qualityMethod"
}
],
"strength": "example",
"description": "The method used to evaluate the numerical quality of the observed sequence.",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/sequence-quality-method|3.0.2"
}
}
},
{
"id": "Sequence.quality.truthTP",
"path": "Sequence.quality.truthTP",
"short": "True positives from the perspective of the truth data",
"definition": "True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quality.truthTP",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.queryTP",
"path": "Sequence.quality.queryTP",
"short": "True positives from the perspective of the query data",
"definition": "True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quality.queryTP",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.truthFN",
"path": "Sequence.quality.truthFN",
"short": "False negatives",
"definition": "False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quality.truthFN",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.queryFP",
"path": "Sequence.quality.queryFP",
"short": "False positives",
"definition": "False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quality.queryFP",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.gtFP",
"path": "Sequence.quality.gtFP",
"short": "False positives where the non-REF alleles in the Truth and Query Call Sets match",
"definition": "The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quality.gtFP",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.precision",
"path": "Sequence.quality.precision",
"short": "Precision of comparison",
"definition": "QUERY.TP / (QUERY.TP + QUERY.FP).",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quality.precision",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.recall",
"path": "Sequence.quality.recall",
"short": "Recall of comparison",
"definition": "TRUTH.TP / (TRUTH.TP + TRUTH.FN).",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quality.recall",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.quality.fScore",
"path": "Sequence.quality.fScore",
"short": "F-score",
"definition": "Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.quality.fScore",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"isSummary": true
},
{
"id": "Sequence.readCoverage",
"path": "Sequence.readCoverage",
"short": "Average number of reads representing a given nucleotide in the reconstructed sequence",
"definition": "Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.readCoverage",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"isSummary": true
},
{
"id": "Sequence.repository",
"path": "Sequence.repository",
"short": "External repository which contains detailed report related with observedSeq in this resource",
"definition": "Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.",
"min": 0,
"max": "*",
"base": {
"path": "Sequence.repository",
"min": 0,
"max": "*"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() | (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isSummary": true
},
{
"id": "Sequence.repository.id",
"path": "Sequence.repository.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.repository.extension",
"path": "Sequence.repository.extension",
"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. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to 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"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.repository.modifierExtension",
"path": "Sequence.repository.modifierExtension",
"short": "Extensions that cannot be ignored",
"definition": "May be used to represent additional information that is not part of the basic definition of the element, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.",
"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",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": true,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.repository.type",
"path": "Sequence.repository.type",
"short": "directlink | openapi | login | oauth | other",
"definition": "Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.",
"min": 1,
"max": "1",
"base": {
"path": "Sequence.repository.type",
"min": 1,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "repositoryType"
}
],
"strength": "required",
"description": "Type for access of external URI",
"valueSetReference": {
"reference": "http://hl7.org/fhir/ValueSet/repository-type|3.0.2"
}
}
},
{
"id": "Sequence.repository.url",
"path": "Sequence.repository.url",
"short": "URI of the repository",
"definition": "URI of an external repository which contains further details about the genetics data.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.repository.url",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"isSummary": true
},
{
"id": "Sequence.repository.name",
"path": "Sequence.repository.name",
"short": "Repository's name",
"definition": "URI of an external repository which contains further details about the genetics data.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.repository.name",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.repository.datasetId",
"path": "Sequence.repository.datasetId",
"short": "Id of the dataset that used to call for dataset in repository",
"definition": "Id of the variant in this external repository. The server will understand how to use this id to call for more info about datasets in external repository.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.repository.datasetId",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.repository.variantsetId",
"path": "Sequence.repository.variantsetId",
"short": "Id of the variantset that used to call for variantset in repository",
"definition": "Id of the variantset in this external repository. The server will understand how to use this id to call for more info about variantsets in external repository.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.repository.variantsetId",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.repository.readsetId",
"path": "Sequence.repository.readsetId",
"short": "Id of the read",
"definition": "Id of the read in this external repository.",
"min": 0,
"max": "1",
"base": {
"path": "Sequence.repository.readsetId",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true
},
{
"id": "Sequence.pointer",
"path": "Sequence.pointer",
"short": "Pointer to next atomic sequence",
"definition": "Pointer to next atomic sequence which at most contains one variant.",
"min": 0,
"max": "*",
"base": {
"path": "Sequence.pointer",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Reference",
"targetProfile": "http://hl7.org/fhir/StructureDefinition/Sequence"
}
],
"isSummary": true
},
{
"id": "Sequence.pointer.id",
"path": "Sequence.pointer.id",
"representation": [
"xmlAttr"
],
"short": "xml:id (or equivalent in JSON)",
"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": [
{
"code": "string"
}
],
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Sequence.pointer.extension",
"path": "Sequence.pointer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.pointer.extension:pointer",
"path": "Sequence.pointer.extension",
"sliceName": "pointer",
"short": "R4B: pointer additional types",
"definition": "R4B: `MolecularSequence.pointer` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.pointer` is mapped to FHIR STU3 element `Sequence.pointer` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.pointer` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.pointer` with unmapped reference targets: MolecularSequence.",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
},
{
"id": "Sequence.pointer.reference",
"path": "Sequence.pointer.reference",
"short": "Literal reference, Relative, internal or absolute URL",
"definition": "A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.",
"comment": "Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure \"/[type]/[id]\" then it should be assumed that the reference is to a FHIR RESTful server.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.reference",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"condition": [
"ref-1"
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Sequence.pointer.identifier",
"path": "Sequence.pointer.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the other resource. This is used when there is no way to reference the other resource directly, either because the entity is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.",
"comment": "When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. \n\nWhen both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference\n\nApplications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "Sequence.pointer.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "Sequence.pointer.display",
"short": "Text alternative for the resource",
"definition": "Plain text narrative that identifies the resource in addition to the resource reference.",
"comment": "This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.display",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
}
]
},
"differential": {
"element": [
{
"id": "Sequence",
"path": "Sequence"
},
{
"id": "Sequence.meta.extension",
"path": "Sequence.meta.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.meta.extension:meta",
"path": "Sequence.meta.extension",
"sliceName": "meta",
"short": "R4B: meta additional types",
"definition": "R4B: `MolecularSequence.meta` additional types (Meta) additional types from child elements (lastUpdated, profile, security, source, tag, versionId)",
"comment": "Element `MolecularSequence.meta` is mapped to FHIR STU3 element `Sequence.meta` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.meta` do not cover the following types: Meta.\nThe mappings for `MolecularSequence.meta` do not cover the following types based on type expansion: lastUpdated, profile, security, source, tag, versionId.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.meta|0.1.0"
}
]
},
{
"id": "Sequence.text.extension",
"path": "Sequence.text.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.text.extension:text",
"path": "Sequence.text.extension",
"sliceName": "text",
"short": "R4B: text additional types",
"definition": "R4B: `MolecularSequence.text` additional types (Narrative) additional types from child elements (div, status)",
"comment": "Element `MolecularSequence.text` is mapped to FHIR STU3 element `Sequence.text` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.text` do not cover the following types: Narrative.\nThe mappings for `MolecularSequence.text` do not cover the following types based on type expansion: div, status.\nContained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a \"text blob\" or where text is additionally entered raw or narrated and encoded information is added later.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.text|0.1.0"
}
]
},
{
"id": "Sequence.extension",
"path": "Sequence.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.extension:structureVariant",
"path": "Sequence.extension",
"sliceName": "structureVariant",
"short": "R4B: Structural variant (new)",
"definition": "R4B: `MolecularSequence.structureVariant` (new:BackboneElement)",
"comment": "Element `MolecularSequence.structureVariant` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.structureVariant` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.structureVariant|0.1.0"
}
]
},
{
"id": "Sequence.identifier.extension",
"path": "Sequence.identifier.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.identifier.extension:identifier",
"path": "Sequence.identifier.extension",
"sliceName": "identifier",
"short": "R4B: identifier additional types",
"definition": "R4B: `MolecularSequence.identifier` additional types (Identifier) additional types from child elements (assigner, period, system, type, use, value)",
"comment": "Element `MolecularSequence.identifier` is mapped to FHIR STU3 element `Sequence.identifier` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.identifier` do not cover the following types: Identifier.\nThe mappings for `MolecularSequence.identifier` do not cover the following types based on type expansion: assigner, period, system, type, use, value.",
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.identifier|0.1.0"
}
]
},
{
"id": "Sequence.type.extension",
"path": "Sequence.type.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.type.extension:type",
"path": "Sequence.type.extension",
"sliceName": "type",
"short": "R4B: type",
"definition": "R4B: `MolecularSequence.type`",
"comment": "Element `MolecularSequence.type` is mapped to FHIR STU3 element `Sequence.type` as `Equivalent`.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.type|0.1.0"
}
]
},
{
"id": "Sequence.patient.extension",
"path": "Sequence.patient.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.patient.extension:patient",
"path": "Sequence.patient.extension",
"sliceName": "patient",
"short": "R4B: patient additional types",
"definition": "R4B: `MolecularSequence.patient` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.patient` is mapped to FHIR STU3 element `Sequence.patient` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.patient` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.patient` with unmapped reference targets: Patient.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
},
{
"id": "Sequence.specimen.extension",
"path": "Sequence.specimen.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.specimen.extension:specimen",
"path": "Sequence.specimen.extension",
"sliceName": "specimen",
"short": "R4B: specimen additional types",
"definition": "R4B: `MolecularSequence.specimen` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.specimen` is mapped to FHIR STU3 element `Sequence.specimen` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.specimen` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.specimen` with unmapped reference targets: Specimen.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
},
{
"id": "Sequence.device.extension",
"path": "Sequence.device.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.device.extension:device",
"path": "Sequence.device.extension",
"sliceName": "device",
"short": "R4B: device additional types",
"definition": "R4B: `MolecularSequence.device` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.device` is mapped to FHIR STU3 element `Sequence.device` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.device` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.device` with unmapped reference targets: Device.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
},
{
"id": "Sequence.performer.extension",
"path": "Sequence.performer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.performer.extension:performer",
"path": "Sequence.performer.extension",
"sliceName": "performer",
"short": "R4B: performer additional types",
"definition": "R4B: `MolecularSequence.performer` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.performer` is mapped to FHIR STU3 element `Sequence.performer` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.performer` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.performer` with unmapped reference targets: Organization.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
},
{
"id": "Sequence.referenceSeq.extension",
"path": "Sequence.referenceSeq.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.referenceSeq.extension:orientation",
"path": "Sequence.referenceSeq.extension",
"sliceName": "orientation",
"short": "R4B: sense | antisense (new)",
"definition": "R4B: `MolecularSequence.referenceSeq.orientation` (new:code)",
"comment": "Element `MolecularSequence.referenceSeq.orientation` has a context of Sequence.referenceSeq based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.referenceSeq.orientation` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.referenceSeq.orientation|0.1.0"
}
]
},
{
"id": "Sequence.referenceSeq.referenceSeqPointer.extension",
"path": "Sequence.referenceSeq.referenceSeqPointer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.referenceSeq.referenceSeqPointer.extension:referenceSeqPointer",
"path": "Sequence.referenceSeq.referenceSeqPointer.extension",
"sliceName": "referenceSeqPointer",
"short": "R4B: A pointer to another MolecularSequence entity as reference sequence additional types",
"definition": "R4B: `MolecularSequence.referenceSeq.referenceSeqPointer` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.referenceSeq.referenceSeqPointer` is mapped to FHIR STU3 element `Sequence.referenceSeq.referenceSeqPointer` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.referenceSeq.referenceSeqPointer` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.referenceSeq.referenceSeqPointer` with unmapped reference targets: MolecularSequence.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
},
{
"id": "Sequence.referenceSeq.strand.extension",
"path": "Sequence.referenceSeq.strand.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.referenceSeq.strand.extension:strand",
"path": "Sequence.referenceSeq.strand.extension",
"sliceName": "strand",
"short": "R4B: watson | crick additional types",
"definition": "R4B: `MolecularSequence.referenceSeq.strand` additional types (code) additional types from child elements (value)",
"comment": "Element `MolecularSequence.referenceSeq.strand` is mapped to FHIR STU3 element `Sequence.referenceSeq.strand` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.referenceSeq.strand` do not cover the following types: code.\nThe mappings for `MolecularSequence.referenceSeq.strand` do not cover the following types based on type expansion: value.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.referenceSeq.strand|0.1.0"
}
]
},
{
"id": "Sequence.variant.variantPointer.extension",
"path": "Sequence.variant.variantPointer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.variant.variantPointer.extension:variantPointer",
"path": "Sequence.variant.variantPointer.extension",
"sliceName": "variantPointer",
"short": "R4B: variantPointer additional types",
"definition": "R4B: `MolecularSequence.variant.variantPointer` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.variant.variantPointer` is mapped to FHIR STU3 element `Sequence.variant.variantPointer` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.variant.variantPointer` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.variant.variantPointer` with unmapped reference targets: Observation.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
},
{
"id": "Sequence.quality.extension",
"path": "Sequence.quality.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.quality.extension:roc",
"path": "Sequence.quality.extension",
"sliceName": "roc",
"short": "R4B: Receiver Operator Characteristic (ROC) Curve (new)",
"definition": "R4B: `MolecularSequence.quality.roc` (new:BackboneElement)",
"comment": "Element `MolecularSequence.quality.roc` has a context of Sequence.quality based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.quality.roc` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.quality.roc|0.1.0"
}
]
},
{
"id": "Sequence.pointer.extension",
"path": "Sequence.pointer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.pointer.extension:pointer",
"path": "Sequence.pointer.extension",
"sliceName": "pointer",
"short": "R4B: pointer additional types",
"definition": "R4B: `MolecularSequence.pointer` additional types from child elements (display, identifier, reference, type)",
"comment": "Element `MolecularSequence.pointer` is mapped to FHIR STU3 element `Sequence.pointer` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.pointer` do not cover the following types based on type expansion: display, identifier, reference, type.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R4B element `MolecularSequence.pointer` with unmapped reference targets: MolecularSequence.",
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/StructureDefinition/alternate-reference"
}
]
}
]
}
}