FHIR IG analytics| Package | hl7.fhir.uv.xver-r5.r3 |
| Resource Type | StructureDefinition |
| Id | StructureDefinition-profile-MolecularSequence-for-Sequence.json |
| FHIR Version | R3 |
| Source | http://hl7.org/fhir/uv/xver-r5.r3/0.1.0/StructureDefinition-profile-MolecularSequence-for-Sequence.html |
| URL | http://hl7.org/fhir/5.0/StructureDefinition/profile-MolecularSequence-for-Sequence |
| Version | 0.1.0 |
| Status | active |
| Date | 2026-03-17T16:05:13.0637646-05:00 |
| Name | Profile_R5_MolecularSequence_R3_Sequence |
| Title | Cross-version Profile for R5.MolecularSequence for use in FHIR STU3 |
| Realm | uv |
| Authority | hl7 |
| Description | This cross-version profile allows R5 MolecularSequence content to be represented via FHIR STU3 Sequence resources. |
| Type | Sequence |
| Kind | resource |
No resources found
| StructureDefinition | ||
| hl7.fhir.uv.xver-r5.r4.r4#0.0.1-snapshot-2 | extension-MolecularSequence.focus | Cross-version Extension for R5.MolecularSequence.focus for use in FHIR R4 |
| hl7.fhir.uv.xver-r5.r4.r4#0.0.1-snapshot-2 | extension-MolecularSequence.formatted | Cross-version Extension for R5.MolecularSequence.formatted for use in FHIR R4 |
| hl7.fhir.uv.xver-r5.r4#0.1.0 | extension-MolecularSequence.relative.coordinateSystem | R5: Ways of identifying nucleotides or amino acids within a sequence (new) |
| hl7.fhir.uv.xver-r5.r4#0.1.0 | extension-MolecularSequence.relative.edit.start | R5: Start position of the edit on the starting sequence (new) |
| hl7.fhir.uv.xver-r5.r4#0.1.0 | extension-MolecularSequence.relative.ordinalPosition | R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new) |
| hl7.fhir.uv.xver-r5.r4#0.1.0 | extension-MolecularSequence.relative.sequenceRange | R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new) |
| hl7.fhir.uv.xver-r5.r4#0.1.0 | extension-MolecularSequence.relative.startingSequence.chromosome | R5: Chromosome Identifier |
| hl7.fhir.uv.xver-r5.r4#0.1.0 | extension-MolecularSequence.relative.startingSequence.genomeAssembly | R5: The genome assembly used for starting sequence, e.g. GRCh38 (new) |
| hl7.fhir.uv.xver-r5.r3#0.1.0 | extension-MolecularSequence.relative.startingSequence.orientation | R5: sense | antisense (new) |
| hl7.fhir.uv.xver-r5.r4#0.1.0 | extension-MolecularSequence.relative.startingSequence.sequence | R5: The reference sequence that represents the starting sequence additional types |
| hl7.fhir.uv.xver-r5.r3#0.1.0 | extension-MolecularSequence.relative.startingSequence.strand | R5: watson | crick additional types |
| hl7.fhir.uv.xver-r5.r3#0.1.0 | extension-MolecularSequence.type | R5: 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 | |
  Slices for extension | 1..* | Extension | Extension Slice: Unordered, Open by value:url | |
   extension:focus | 0..* | Reference(Cross-version Profile for R5.Resource for use in FHIR STU3(0.1.0) | Resource) | R5: What the molecular sequence is about, when it is not about the subject of record (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.focus | |
| extension:formatted | 0..* | Attachment | R5: Embedded file or a link (URL) which contains content to represent the sequence (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.formatted | |
| extension:coordinateSystem | 1..1 | CodeableConcept | R5: Ways of identifying nucleotides or amino acids within a sequence (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem | |
| extension:ordinalPosition | 0..1 | integer | R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition | |
 extension:sequenceRange | 0..1 | Range | R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange | |
 type | ||||
 Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
 extension:type | 0..1 | code | R5: type URL: http://hl7.org/fhir/5.0/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:subject | 0..1 | ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] | R5: Subject this sequence is associated too 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]] | R5: 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]] | R5: 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]] | R5: 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:genomeAssembly | 0..1 | CodeableConcept | R5: The genome assembly used for starting sequence, e.g. GRCh38 (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.genomeAssembly | |
| extension:sequence | 0..1 | CodeableConcept, Reference(Cross-version Profile for R5.MolecularSequence for use in FHIR STU3(0.1.0) | Sequence) | R5: The reference sequence that represents the starting sequence additional types URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence | |
| extension:orientation | 0..1 | code | R5: sense | antisense (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.orientation Binding: R5OrientationTypeForR3 (0.1.0) (required): Type for orientation | |
| chromosome | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:chromosome | 0..1 | CodeableConcept | R5: Chromosome Identifier URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome | |
| strand | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:strand | 0..1 | code | R5: watson | crick additional types URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.strand Binding: R5StrandTypeForR3 (0.1.0) (required): Type for strand | |
| variant | ||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:start | 0..1 | integer | R5: Start position of the edit on the starting sequence (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.edit.start | |
| 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-r5.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-r5.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-r5.r3"
}
]
}
}
],
"url": "http://hl7.org/fhir/5.0/StructureDefinition/profile-MolecularSequence-for-Sequence",
"version": "0.1.0",
"name": "Profile_R5_MolecularSequence_R3_Sequence",
"title": "Cross-version Profile for R5.MolecularSequence for use in FHIR STU3",
"status": "active",
"experimental": false,
"date": "2026-03-17T16:05:13.0637646-05:00",
"publisher": "FHIR Infrastructure",
"contact": [
{
"name": "FHIR Infrastructure",
"telecom": [
{
"system": "url",
"value": "http://www.hl7.org/Special/committees/fiwg"
}
]
}
],
"description": "This cross-version profile allows R5 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.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.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": 1,
"max": "*",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Sequence.extension:focus",
"path": "Sequence.extension",
"sliceName": "focus",
"short": "R5: What the molecular sequence is about, when it is not about the subject of record (new)",
"definition": "R5: `MolecularSequence.focus` (new:Reference(Resource))",
"comment": "Element `MolecularSequence.focus` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.focus` 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/5.0/StructureDefinition/extension-MolecularSequence.focus|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.extension:formatted",
"path": "Sequence.extension",
"sliceName": "formatted",
"short": "R5: Embedded file or a link (URL) which contains content to represent the sequence (new)",
"definition": "R5: `MolecularSequence.formatted` (new:Attachment)",
"comment": "Element `MolecularSequence.formatted` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.formatted` 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/5.0/StructureDefinition/extension-MolecularSequence.formatted|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.extension:coordinateSystem",
"path": "Sequence.extension",
"sliceName": "coordinateSystem",
"short": "R5: Ways of identifying nucleotides or amino acids within a sequence (new)",
"definition": "R5: `MolecularSequence.relative.coordinateSystem` (new:CodeableConcept)",
"comment": "Element `MolecularSequence.relative.coordinateSystem` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.relative.coordinateSystem` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).",
"min": 1,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem|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.extension:ordinalPosition",
"path": "Sequence.extension",
"sliceName": "ordinalPosition",
"short": "R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new)",
"definition": "R5: `MolecularSequence.relative.ordinalPosition` (new:integer)",
"comment": "Element `MolecularSequence.relative.ordinalPosition` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.relative.ordinalPosition` 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/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition|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.extension:sequenceRange",
"path": "Sequence.extension",
"sliceName": "sequenceRange",
"short": "R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new)",
"definition": "R5: `MolecularSequence.relative.sequenceRange` (new:Range)",
"comment": "Element `MolecularSequence.relative.sequenceRange` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.relative.sequenceRange` 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/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange|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.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": "R5: type",
"definition": "R5: `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/5.0/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:subject",
"path": "Sequence.patient.extension",
"sliceName": "subject",
"short": "R5: Subject this sequence is associated too",
"definition": "R5: `MolecularSequence.subject`",
"comment": "Element `MolecularSequence.subject` is mapped to FHIR STU3 element `Sequence.patient` as `SourceIsBroaderThanTarget`.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `MolecularSequence.subject` with unmapped reference targets: BiologicallyDerivedProduct, Group, NutritionProduct, Patient, Substance.",
"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": "R5: specimen additional types",
"definition": "R5: `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 R5 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": "R5: device additional types",
"definition": "R5: `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 R5 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": "R5: performer additional types",
"definition": "R5: `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 R5 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:genomeAssembly",
"path": "Sequence.referenceSeq.extension",
"sliceName": "genomeAssembly",
"short": "R5: The genome assembly used for starting sequence, e.g. GRCh38 (new)",
"definition": "R5: `MolecularSequence.relative.startingSequence.genomeAssembly` (new:CodeableConcept)",
"comment": "Element `MolecularSequence.relative.startingSequence.genomeAssembly` has a context of Sequence.referenceSeq based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.relative.startingSequence.genomeAssembly` 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/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.genomeAssembly|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.extension:sequence",
"path": "Sequence.referenceSeq.extension",
"sliceName": "sequence",
"short": "R5: The reference sequence that represents the starting sequence additional types",
"definition": "R5: `MolecularSequence.relative.startingSequence.sequence[x]` additional types (CodeableConcept, Reference(http://hl7.org/fhir/StructureDefinition/MolecularSequence))",
"comment": "Element `MolecularSequence.relative.startingSequence.sequence[x]` is mapped to FHIR STU3 element `Sequence.referenceSeq.referenceSeqString` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.relative.startingSequence.sequence[x]` do not cover the following types: CodeableConcept, Reference.\nA starting sequence may be represented in one of three ways:\n 1. CodeableConcept, using NCBI, LRG or other appropriate code systems\n 1. a simple string of IUPAC codes\n 1. a reference to another MolecularSequence resource.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence|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.extension:orientation",
"path": "Sequence.referenceSeq.extension",
"sliceName": "orientation",
"short": "R5: sense | antisense (new)",
"definition": "R5: `MolecularSequence.relative.startingSequence.orientation` (new:code)",
"comment": "Element `MolecularSequence.relative.startingSequence.orientation` has a context of Sequence.referenceSeq based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.relative.startingSequence.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/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.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.chromosome.id",
"path": "Sequence.referenceSeq.chromosome.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.chromosome.extension",
"path": "Sequence.referenceSeq.chromosome.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.chromosome.extension:chromosome",
"path": "Sequence.referenceSeq.chromosome.extension",
"sliceName": "chromosome",
"short": "R5: Chromosome Identifier",
"definition": "R5: `MolecularSequence.relative.startingSequence.chromosome`",
"comment": "Element `MolecularSequence.relative.startingSequence.chromosome` is mapped to FHIR STU3 element `Sequence.referenceSeq.chromosome` as `Equivalent`.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome|0.1.0"
}
]
},
{
"id": "Sequence.referenceSeq.chromosome.coding",
"path": "Sequence.referenceSeq.chromosome.coding",
"short": "Code defined by a terminology system",
"definition": "A reference to a code defined by a terminology system.",
"comment": "Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.",
"requirements": "Allows for translations and alternate encodings within a code system. Also supports communication of the same instance to systems requiring different encodings.",
"min": 0,
"max": "*",
"base": {
"path": "CodeableConcept.coding",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Coding"
}
],
"isSummary": true,
"mapping": [
{
"identity": "v2",
"map": "C*E.1-8, C*E.10-22"
},
{
"identity": "rim",
"map": "union(., ./translation)"
},
{
"identity": "orim",
"map": "fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding"
}
]
},
{
"id": "Sequence.referenceSeq.chromosome.text",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "Sequence.referenceSeq.chromosome.text",
"short": "Plain text representation of the concept",
"definition": "A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.",
"comment": "Very often the text is the same as a displayName of one of the codings.",
"requirements": "The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source.",
"min": 0,
"max": "1",
"base": {
"path": "CodeableConcept.text",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"isSummary": true,
"mapping": [
{
"identity": "v2",
"map": "C*E.9. But note many systems use C*E.2 for this"
},
{
"identity": "rim",
"map": "./originalText[mediaType/code=\"text/plain\"]/data"
},
{
"identity": "orim",
"map": "fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText"
}
]
},
{
"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.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": "R5: watson | crick additional types",
"definition": "R5: `MolecularSequence.relative.startingSequence.strand` additional types (code) additional types from child elements (value)",
"comment": "Element `MolecularSequence.relative.startingSequence.strand` is mapped to FHIR STU3 element `Sequence.referenceSeq.strand` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.relative.startingSequence.strand` do not cover the following types: code.\nThe mappings for `MolecularSequence.relative.startingSequence.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/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.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",
"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.variant.extension:start",
"path": "Sequence.variant.extension",
"sliceName": "start",
"short": "R5: Start position of the edit on the starting sequence (new)",
"definition": "R5: `MolecularSequence.relative.edit.start` (new:integer)",
"comment": "Element `MolecularSequence.relative.edit.start` has a context of Sequence.variant based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.relative.edit.start` 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/5.0/StructureDefinition/extension-MolecularSequence.relative.edit.start|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.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.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",
"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.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
}
]
},
"differential": {
"element": [
{
"id": "Sequence",
"path": "Sequence"
},
{
"id": "Sequence.extension",
"path": "Sequence.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 1,
"max": "*"
},
{
"id": "Sequence.extension:focus",
"path": "Sequence.extension",
"sliceName": "focus",
"short": "R5: What the molecular sequence is about, when it is not about the subject of record (new)",
"definition": "R5: `MolecularSequence.focus` (new:Reference(Resource))",
"comment": "Element `MolecularSequence.focus` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.focus` 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/5.0/StructureDefinition/extension-MolecularSequence.focus|0.1.0"
}
]
},
{
"id": "Sequence.extension:formatted",
"path": "Sequence.extension",
"sliceName": "formatted",
"short": "R5: Embedded file or a link (URL) which contains content to represent the sequence (new)",
"definition": "R5: `MolecularSequence.formatted` (new:Attachment)",
"comment": "Element `MolecularSequence.formatted` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.formatted` 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/5.0/StructureDefinition/extension-MolecularSequence.formatted|0.1.0"
}
]
},
{
"id": "Sequence.extension:coordinateSystem",
"path": "Sequence.extension",
"sliceName": "coordinateSystem",
"short": "R5: Ways of identifying nucleotides or amino acids within a sequence (new)",
"definition": "R5: `MolecularSequence.relative.coordinateSystem` (new:CodeableConcept)",
"comment": "Element `MolecularSequence.relative.coordinateSystem` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.relative.coordinateSystem` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).",
"min": 1,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem|0.1.0"
}
]
},
{
"id": "Sequence.extension:ordinalPosition",
"path": "Sequence.extension",
"sliceName": "ordinalPosition",
"short": "R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new)",
"definition": "R5: `MolecularSequence.relative.ordinalPosition` (new:integer)",
"comment": "Element `MolecularSequence.relative.ordinalPosition` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.relative.ordinalPosition` 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/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition|0.1.0"
}
]
},
{
"id": "Sequence.extension:sequenceRange",
"path": "Sequence.extension",
"sliceName": "sequenceRange",
"short": "R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new)",
"definition": "R5: `MolecularSequence.relative.sequenceRange` (new:Range)",
"comment": "Element `MolecularSequence.relative.sequenceRange` has a context of Sequence based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.relative.sequenceRange` 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/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange|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": "R5: type",
"definition": "R5: `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/5.0/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:subject",
"path": "Sequence.patient.extension",
"sliceName": "subject",
"short": "R5: Subject this sequence is associated too",
"definition": "R5: `MolecularSequence.subject`",
"comment": "Element `MolecularSequence.subject` is mapped to FHIR STU3 element `Sequence.patient` as `SourceIsBroaderThanTarget`.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `MolecularSequence.subject` with unmapped reference targets: BiologicallyDerivedProduct, Group, NutritionProduct, Patient, Substance.",
"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": "R5: specimen additional types",
"definition": "R5: `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 R5 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": "R5: device additional types",
"definition": "R5: `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 R5 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": "R5: performer additional types",
"definition": "R5: `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 R5 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:genomeAssembly",
"path": "Sequence.referenceSeq.extension",
"sliceName": "genomeAssembly",
"short": "R5: The genome assembly used for starting sequence, e.g. GRCh38 (new)",
"definition": "R5: `MolecularSequence.relative.startingSequence.genomeAssembly` (new:CodeableConcept)",
"comment": "Element `MolecularSequence.relative.startingSequence.genomeAssembly` has a context of Sequence.referenceSeq based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.relative.startingSequence.genomeAssembly` 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/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.genomeAssembly|0.1.0"
}
]
},
{
"id": "Sequence.referenceSeq.extension:sequence",
"path": "Sequence.referenceSeq.extension",
"sliceName": "sequence",
"short": "R5: The reference sequence that represents the starting sequence additional types",
"definition": "R5: `MolecularSequence.relative.startingSequence.sequence[x]` additional types (CodeableConcept, Reference(http://hl7.org/fhir/StructureDefinition/MolecularSequence))",
"comment": "Element `MolecularSequence.relative.startingSequence.sequence[x]` is mapped to FHIR STU3 element `Sequence.referenceSeq.referenceSeqString` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.relative.startingSequence.sequence[x]` do not cover the following types: CodeableConcept, Reference.\nA starting sequence may be represented in one of three ways:\n 1. CodeableConcept, using NCBI, LRG or other appropriate code systems\n 1. a simple string of IUPAC codes\n 1. a reference to another MolecularSequence resource.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence|0.1.0"
}
]
},
{
"id": "Sequence.referenceSeq.extension:orientation",
"path": "Sequence.referenceSeq.extension",
"sliceName": "orientation",
"short": "R5: sense | antisense (new)",
"definition": "R5: `MolecularSequence.relative.startingSequence.orientation` (new:code)",
"comment": "Element `MolecularSequence.relative.startingSequence.orientation` has a context of Sequence.referenceSeq based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.relative.startingSequence.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/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.orientation|0.1.0"
}
]
},
{
"id": "Sequence.referenceSeq.chromosome.extension",
"path": "Sequence.referenceSeq.chromosome.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.referenceSeq.chromosome.extension:chromosome",
"path": "Sequence.referenceSeq.chromosome.extension",
"sliceName": "chromosome",
"short": "R5: Chromosome Identifier",
"definition": "R5: `MolecularSequence.relative.startingSequence.chromosome`",
"comment": "Element `MolecularSequence.relative.startingSequence.chromosome` is mapped to FHIR STU3 element `Sequence.referenceSeq.chromosome` as `Equivalent`.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": "http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome|0.1.0"
}
]
},
{
"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": "R5: watson | crick additional types",
"definition": "R5: `MolecularSequence.relative.startingSequence.strand` additional types (code) additional types from child elements (value)",
"comment": "Element `MolecularSequence.relative.startingSequence.strand` is mapped to FHIR STU3 element `Sequence.referenceSeq.strand` as `SourceIsBroaderThanTarget`.\nThe mappings for `MolecularSequence.relative.startingSequence.strand` do not cover the following types: code.\nThe mappings for `MolecularSequence.relative.startingSequence.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/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.strand|0.1.0"
}
]
},
{
"id": "Sequence.variant.extension",
"path": "Sequence.variant.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "Sequence.variant.extension:start",
"path": "Sequence.variant.extension",
"sliceName": "start",
"short": "R5: Start position of the edit on the starting sequence (new)",
"definition": "R5: `MolecularSequence.relative.edit.start` (new:integer)",
"comment": "Element `MolecularSequence.relative.edit.start` has a context of Sequence.variant based on following the parent source element upwards and mapping to `Sequence`.\nElement `MolecularSequence.relative.edit.start` 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/5.0/StructureDefinition/extension-MolecularSequence.relative.edit.start|0.1.0"
}
]
}
]
}
}