FHIR IG analytics| Package | hl7.fhir.uv.xver-r3.r4b |
| Resource Type | StructureDefinition |
| Id | StructureDefinition-profile-Sequence-for-MolecularSequence.json |
| FHIR Version | R4B |
| Source | http://hl7.org/fhir/uv/xver-r3.r4b/0.1.0/StructureDefinition-profile-Sequence-for-MolecularSequence.html |
| URL | http://hl7.org/fhir/3.0/StructureDefinition/profile-Sequence-for-MolecularSequence |
| Version | 0.1.0 |
| Status | active |
| Date | 2026-03-17T16:04:10.3485067-05:00 |
| Name | Profile_R3_Sequence_R4B_MolecularSequence |
| Title | Cross-version Profile for STU3.Sequence for use in FHIR R4B |
| Realm | uv |
| Authority | hl7 |
| Description | This cross-version profile allows STU3 Sequence content to be represented via FHIR R4B MolecularSequence resources. |
| Type | MolecularSequence |
| Kind | resource |
No resources found
| StructureDefinition | ||
| hl7.fhir.uv.xver-r3.r4b#0.1.0 | extension-Sequence.identifier | STU3: identifier additional types |
| hl7.fhir.uv.xver-r3.r4b#0.1.0 | extension-Sequence.meta | STU3: meta additional types |
| hl7.fhir.uv.xver-r3.r4b#0.1.0 | extension-Sequence.referenceSeq.strand | STU3: Directionality of DNA ( +1/-1) additional types |
| hl7.fhir.uv.xver-r3.r4b#0.1.0 | extension-Sequence.text | STU3: text additional types |
Note: links and images are rebased to the (stated) source
Generated Narrative: StructureDefinition profile-Sequence-for-MolecularSequence
FHIR
FHIRsmith
{
"resourceType": "StructureDefinition",
"id": "profile-Sequence-for-MolecularSequence",
"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-r3.r4b"
},
{
"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",
"valueCanonical": "http://hl7.org/fhir/uv/xver/ImplementationGuide/hl7.fhir.uv.xver-r3.r4b"
}
]
}
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
"valueCode": "trial-use",
"_valueCode": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
"valueCanonical": "http://hl7.org/fhir/uv/xver/ImplementationGuide/hl7.fhir.uv.xver-r3.r4b"
}
]
}
}
],
"url": "http://hl7.org/fhir/3.0/StructureDefinition/profile-Sequence-for-MolecularSequence",
"version": "0.1.0",
"name": "Profile_R3_Sequence_R4B_MolecularSequence",
"title": "Cross-version Profile for STU3.Sequence for use in FHIR R4B",
"status": "active",
"experimental": false,
"date": "2026-03-17T16:04:10.3485067-05:00",
"publisher": "FHIR Infrastructure",
"contact": [
{
"name": "FHIR Infrastructure",
"telecom": [
{
"system": "url",
"value": "http://www.hl7.org/Special/committees/fiwg"
}
]
}
],
"description": "This cross-version profile allows STU3 Sequence content to be represented via FHIR R4B MolecularSequence resources.",
"jurisdiction": [
{
"coding": [
{
"system": "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code": "001",
"display": "World"
}
]
}
],
"fhirVersion": "4.3.0",
"mapping": [
{
"identity": "w5",
"uri": "http://hl7.org/fhir/fivews",
"name": "FiveWs Pattern Mapping"
},
{
"identity": "rim",
"uri": "http://hl7.org/v3",
"name": "RIM Mapping"
}
],
"kind": "resource",
"abstract": false,
"type": "MolecularSequence",
"baseDefinition": "http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.3.0",
"derivation": "constraint",
"snapshot": {
"extension": [
{
"url": "http://hl7.org/fhir/tools/StructureDefinition/snapshot-base-version",
"valueString": "4.3.0"
}
],
"element": [
{
"id": "MolecularSequence",
"path": "MolecularSequence",
"short": "Information about a biological sequence",
"definition": "Raw data describing a biological sequence.",
"min": 0,
"max": "*",
"base": {
"path": "MolecularSequence",
"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|4.3.0"
},
{
"key": "dom-3",
"severity": "error",
"human": "If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource",
"expression": "contained.where(((id.exists() and ('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url)))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(uri) = '#').exists()).not()).trace('unmatched', id).empty()",
"xpath": "not(exists(for $contained in f:contained return $contained[not(exists(parent::*/descendant::f:reference/@value=concat('#', $contained/*/f:id/@value)) or exists(descendant::f:reference[@value='#']))]))",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource|4.3.0"
},
{
"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|4.3.0"
},
{
"key": "dom-5",
"severity": "error",
"human": "If a resource is contained in another resource, it SHALL NOT have a security label",
"expression": "contained.meta.security.empty()",
"xpath": "not(exists(f:contained/*/f:meta/f:security))",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource|4.3.0"
},
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice",
"valueBoolean": true
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice-explanation",
"valueMarkdown": "When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time."
}
],
"key": "dom-6",
"severity": "warning",
"human": "A resource should have narrative for robust management",
"expression": "text.`div`.exists()",
"xpath": "exists(f:text/h:div)",
"source": "http://hl7.org/fhir/StructureDefinition/DomainResource|4.3.0"
},
{
"key": "msq-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/MolecularSequence|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "Entity. Role, or Act"
},
{
"identity": "w5",
"map": "clinical.diagnostics"
}
]
},
{
"id": "MolecularSequence.id",
"path": "MolecularSequence.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": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.meta",
"path": "MolecularSequence.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 might 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"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.meta.id",
"path": "MolecularSequence.meta.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.meta.extension",
"path": "MolecularSequence.meta.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.meta.extension:meta",
"path": "MolecularSequence.meta.extension",
"sliceName": "meta",
"short": "STU3: meta additional types",
"definition": "STU3: `Sequence.meta` additional types (Meta) additional types from child elements (lastUpdated, profile, security, tag, versionId)",
"comment": "Element `Sequence.meta` is mapped to FHIR R4B element `MolecularSequence.meta` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.meta` do not cover the following types: Meta.\nThe mappings for `Sequence.meta` do not cover the following types based on type expansion: lastUpdated, profile, security, tag, versionId.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.meta|0.1.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.meta.versionId",
"path": "MolecularSequence.meta.versionId",
"short": "Version specific identifier",
"definition": "The version specific identifier, as it appears in the version portion of the URL. This value changes when the resource is created, updated, or deleted.",
"comment": "The server assigns this value, and ignores what the client specifies, except in the case that the server is imposing version integrity on updates/deletes.",
"min": 0,
"max": "1",
"base": {
"path": "Meta.versionId",
"min": 0,
"max": "1"
},
"type": [
{
"code": "id"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.meta.lastUpdated",
"path": "MolecularSequence.meta.lastUpdated",
"short": "When the resource version last changed",
"definition": "When the resource last changed - e.g. when the version changed.",
"comment": "This value is always populated except when the resource is first being created. The server / resource manager sets this value; what a client provides is irrelevant. This is equivalent to the HTTP Last-Modified and SHOULD have the same value on a [read](http://hl7.org/fhir/R4B/http.html#read) interaction.",
"min": 0,
"max": "1",
"base": {
"path": "Meta.lastUpdated",
"min": 0,
"max": "1"
},
"type": [
{
"code": "instant"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.meta.source",
"path": "MolecularSequence.meta.source",
"short": "Identifies where the resource comes from",
"definition": "A uri that identifies the source system of the resource. This provides a minimal amount of [Provenance](http://hl7.org/fhir/R4B/provenance.html#) information that can be used to track or differentiate the source of information in the resource. The source may identify another FHIR server, document, message, database, etc.",
"comment": "In the provenance resource, this corresponds to Provenance.entity.what[x]. The exact use of the source (and the implied Provenance.entity.role) is left to implementer discretion. Only one nominated source is allowed; for additional provenance details, a full Provenance resource should be used. \n\nThis element can be used to indicate where the current master source of a resource that has a canonical URL if the resource is no longer hosted at the canonical URL.",
"min": 0,
"max": "1",
"base": {
"path": "Meta.source",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.meta.profile",
"path": "MolecularSequence.meta.profile",
"short": "Profiles this resource claims to conform to",
"definition": "A list of profiles (references to [StructureDefinition](http://hl7.org/fhir/R4B/structuredefinition.html#) resources) that this resource claims to conform to. The URL is a reference to [StructureDefinition.url](http://hl7.org/fhir/R4B/structuredefinition-definitions.html#StructureDefinition.url).",
"comment": "It is up to the server and/or other infrastructure of policy to determine whether/how these claims are verified and/or updated over time. The list of profile URLs is a set.",
"min": 0,
"max": "*",
"base": {
"path": "Meta.profile",
"min": 0,
"max": "*"
},
"type": [
{
"code": "canonical",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/StructureDefinition|4.3.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.meta.security",
"path": "MolecularSequence.meta.security",
"short": "Security Labels applied to this resource",
"definition": "Security labels applied to this resource. These tags connect specific resources to the overall security policy and infrastructure.",
"comment": "The security labels can be updated without changing the stated version of the resource. The list of security labels is a set. Uniqueness is based the system/code, and version and display are ignored.",
"min": 0,
"max": "*",
"base": {
"path": "Meta.security",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Coding"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/binding-definition",
"valueString": "Security Labels from the Healthcare Privacy and Security Classification System."
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "SecurityLabels"
}
],
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/security-labels|4.3.0"
}
},
{
"id": "MolecularSequence.meta.tag",
"path": "MolecularSequence.meta.tag",
"short": "Tags applied to this resource",
"definition": "Tags applied to this resource. Tags are intended to be used to identify and relate resources to process and workflow, and applications are not required to consider the tags when interpreting the meaning of a resource.",
"comment": "The tags can be updated without changing the stated version of the resource. The list of tags is a set. Uniqueness is based the system/code, and version and display are ignored.",
"min": 0,
"max": "*",
"base": {
"path": "Meta.tag",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Coding"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/binding-definition",
"valueString": "Codes that represent various types of tags, commonly workflow-related; e.g. \"Needs review by Dr. Jones\"."
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "Tags"
}
],
"strength": "example",
"valueSet": "http://hl7.org/fhir/ValueSet/common-tags|4.3.0"
}
},
{
"id": "MolecularSequence.implicitRules",
"path": "MolecularSequence.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. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.",
"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. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.",
"min": 0,
"max": "1",
"base": {
"path": "Resource.implicitRules",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": true,
"isModifierReason": "This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation",
"isSummary": true
},
{
"id": "MolecularSequence.language",
"path": "MolecularSequence.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"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": false,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet",
"valueCanonical": "http://hl7.org/fhir/ValueSet/all-languages|4.3.0"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "Language"
}
],
"strength": "preferred",
"description": "IETF language tag",
"valueSet": "http://hl7.org/fhir/ValueSet/languages|4.3.0"
}
},
{
"id": "MolecularSequence.text",
"path": "MolecularSequence.text",
"short": "Text summary of the resource, for human interpretation",
"definition": "A human-readable narrative that contains a summary of the resource and can 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 information is added later.",
"alias": [
"narrative",
"html",
"xhtml",
"display"
],
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.text",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Narrative"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "Act.text?"
}
]
},
{
"id": "MolecularSequence.text.id",
"path": "MolecularSequence.text.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.text.extension",
"path": "MolecularSequence.text.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.text.extension:text",
"path": "MolecularSequence.text.extension",
"sliceName": "text",
"short": "STU3: text additional types",
"definition": "STU3: `Sequence.text` additional types (Narrative) additional types from child elements (div, status)",
"comment": "Element `Sequence.text` is mapped to FHIR R4B element `MolecularSequence.text` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.text` do not cover the following types: Narrative.\nThe mappings for `Sequence.text` do not cover the following types based on type expansion: div, status.\nContained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a \"text blob\" or where text is additionally entered raw or narrated and encoded in formation is added later.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.text|0.1.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.text.status",
"path": "MolecularSequence.text.status",
"short": "generated | extensions | additional | empty",
"definition": "The status of the narrative - whether it's entirely generated (from just the defined data or the extensions too), or whether a human authored it and it may contain additional data.",
"min": 1,
"max": "1",
"base": {
"path": "Narrative.status",
"min": 1,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": false,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/binding-definition",
"valueString": "The status of a resource narrative."
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "NarrativeStatus"
}
],
"strength": "required",
"valueSet": "http://hl7.org/fhir/ValueSet/narrative-status|4.3.0"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.text.div",
"path": "MolecularSequence.text.div",
"short": "Limited xhtml content",
"definition": "The actual narrative content, a stripped down version of XHTML.",
"comment": "The contents of the html element are an XHTML fragment containing only the basic html formatting elements described in chapters 7-11 and 15 of the HTML 4.0 standard, <a> elements (either name or href), images and internally contained stylesheets. The XHTML content SHALL NOT contain a head, a body, external stylesheet references, scripts, forms, base/link/xlink, frames, iframes and objects.",
"min": 1,
"max": "1",
"base": {
"path": "Narrative.div",
"min": 1,
"max": "1"
},
"type": [
{
"code": "xhtml"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"key": "txt-1",
"severity": "error",
"human": "The narrative SHALL contain only the basic html formatting elements and attributes described in chapters 7-11 (except section 4 of chapter 9) and 15 of the HTML 4.0 standard, <a> elements (either name or href), images and internally contained style attributes",
"expression": "htmlChecks()",
"xpath": "not(descendant-or-self::*[not(local-name(.)=('a', 'abbr', 'acronym', 'b', 'big', 'blockquote', 'br', 'caption', 'cite', 'code', 'col', 'colgroup', 'dd', 'dfn', 'div', 'dl', 'dt', 'em', 'h1', 'h2', 'h3', 'h4', 'h5', 'h6', 'hr', 'i', 'img', 'li', 'ol', 'p', 'pre', 'q', 'samp', 'small', 'span', 'strong', 'sub', 'sup', 'table', 'tbody', 'td', 'tfoot', 'th', 'thead', 'tr', 'tt', 'ul', 'var'))]) and not(descendant-or-self::*/@*[not(name(.)=('abbr', 'accesskey', 'align', 'alt', 'axis', 'bgcolor', 'border', 'cellhalign', 'cellpadding', 'cellspacing', 'cellvalign', 'char', 'charoff', 'charset', 'cite', 'class', 'colspan', 'compact', 'coords', 'dir', 'frame', 'headers', 'height', 'href', 'hreflang', 'hspace', 'id', 'lang', 'longdesc', 'name', 'nowrap', 'rel', 'rev', 'rowspan', 'rules', 'scope', 'shape', 'span', 'src', 'start', 'style', 'summary', 'tabindex', 'title', 'type', 'valign', 'value', 'vspace', 'width'))])",
"source": "http://hl7.org/fhir/StructureDefinition/Narrative|4.3.0"
},
{
"key": "txt-2",
"severity": "error",
"human": "The narrative SHALL have some non-whitespace content",
"expression": "htmlChecks()",
"xpath": "descendant::text()[normalize-space(.)!=''] or descendant::h:img[@src]",
"source": "http://hl7.org/fhir/StructureDefinition/Narrative|4.3.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.contained",
"path": "MolecularSequence.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. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.",
"alias": [
"inline resources",
"anonymous resources",
"contained resources"
],
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.contained",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Resource"
}
],
"constraint": [
{
"key": "dom-r4b",
"severity": "warning",
"human": "Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems",
"expression": "($this is Citation or $this is Evidence or $this is EvidenceReport or $this is EvidenceVariable or $this is MedicinalProductDefinition or $this is PackagedProductDefinition or $this is AdministrableProductDefinition or $this is Ingredient or $this is ClinicalUseDefinition or $this is RegulatedAuthorization or $this is SubstanceDefinition or $this is SubscriptionStatus or $this is SubscriptionTopic) implies (%resource is Citation or %resource is Evidence or %resource is EvidenceReport or %resource is EvidenceVariable or %resource is MedicinalProductDefinition or %resource is PackagedProductDefinition or %resource is AdministrableProductDefinition or %resource is Ingredient or %resource is ClinicalUseDefinition or %resource is RegulatedAuthorization or %resource is SubstanceDefinition or %resource is SubscriptionStatus or %resource is SubscriptionTopic)",
"xpath": "not(f:Citation|f:Evidence|f:EvidenceReport|f:EvidenceVariable|f:MedicinalProductDefinition|f:PackagedProductDefinition|f:AdministrableProductDefinition|f:Ingredient|f:ClinicalUseDefinition|f:RegulatedAuthorization|f:SubstanceDefinition|f:SubscriptionStatus|f:SubscriptionTopic) or not(parent::f:Citation|parent::f:Evidence|parent::f:EvidenceReport|parent::f:EvidenceVariable|parent::f:MedicinalProductDefinition|parent::f:PackagedProductDefinition|parent::f:AdministrableProductDefinition|parent::f:Ingredient|parent::f:ClinicalUseDefinition|parent::f:RegulatedAuthorization|parent::f:SubstanceDefinition|f:SubscriptionStatus|f:SubscriptionTopic)",
"source": "http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.extension",
"path": "MolecularSequence.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 resource. 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 can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.modifierExtension",
"path": "MolecularSequence.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 and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"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.",
"requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4B/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"mustSupport": false,
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them",
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.identifier",
"path": "MolecularSequence.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": "MolecularSequence.identifier",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Identifier"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "w5",
"map": "FiveWs.identifier"
}
]
},
{
"id": "MolecularSequence.identifier.id",
"path": "MolecularSequence.identifier.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.identifier.extension",
"path": "MolecularSequence.identifier.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.identifier.extension:identifier",
"path": "MolecularSequence.identifier.extension",
"sliceName": "identifier",
"short": "STU3: identifier additional types",
"definition": "STU3: `Sequence.identifier` additional types (Identifier) additional types from child elements (assigner, period, system, type, use, value)",
"comment": "Element `Sequence.identifier` is mapped to FHIR R4B element `MolecularSequence.identifier` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.identifier` do not cover the following types: Identifier.\nThe mappings for `Sequence.identifier` do not cover the following types based on type expansion: assigner, period, system, type, use, value.",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.identifier|0.1.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.identifier.use",
"path": "MolecularSequence.identifier.use",
"short": "usual | official | temp | secondary | old (If known)",
"definition": "The purpose of this identifier.",
"comment": "Applications can assume that an identifier is permanent unless it explicitly says that it is temporary.",
"requirements": "Allows the appropriate identifier for a particular context of use to be selected from among a set of identifiers.",
"min": 0,
"max": "1",
"base": {
"path": "Identifier.use",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": true,
"isModifierReason": "This is labeled as \"Is Modifier\" because applications should not mistake a temporary id for a permanent one.",
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/binding-definition",
"valueString": "Identifies the purpose for this identifier, if known ."
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "IdentifierUse"
}
],
"strength": "required",
"valueSet": "http://hl7.org/fhir/ValueSet/identifier-use|4.3.0"
},
"mapping": [
{
"identity": "v2",
"map": "N/A"
},
{
"identity": "rim",
"map": "Role.code or implied by context"
}
]
},
{
"id": "MolecularSequence.identifier.type",
"path": "MolecularSequence.identifier.type",
"short": "Description of identifier",
"definition": "A coded type for the identifier that can be used to determine which identifier to use for a specific purpose.",
"comment": "This element deals only with general categories of identifiers. It SHOULD not be used for codes that correspond 1..1 with the Identifier.system. Some identifiers may fall into multiple categories due to common usage. Where the system is known, a type is unnecessary because the type is always part of the system definition. However systems often need to handle identifiers where the system is not known. There is not a 1:1 relationship between type and system, since many different systems have the same type.",
"requirements": "Allows users to make use of identifiers when the identifier system is not known.",
"min": 0,
"max": "1",
"base": {
"path": "Identifier.type",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/binding-definition",
"valueString": "A coded type for an identifier that can be used to determine which identifier to use for a specific purpose."
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "IdentifierType"
}
],
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/identifier-type|4.3.0"
},
"mapping": [
{
"identity": "v2",
"map": "CX.5"
},
{
"identity": "rim",
"map": "Role.code or implied by context"
}
]
},
{
"id": "MolecularSequence.identifier.system",
"path": "MolecularSequence.identifier.system",
"short": "The namespace for the identifier value",
"definition": "Establishes the namespace for the value - that is, a URL that describes a set values that are unique.",
"comment": "Identifier.system is always case sensitive.",
"requirements": "There are many sets of identifiers. To perform matching of two identifiers, we need to know what set we're dealing with. The system identifies a particular set of unique identifiers.",
"min": 0,
"max": "1",
"base": {
"path": "Identifier.system",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"example": [
{
"label": "General",
"valueUri": "http://www.acme.com/identifiers/patient"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "v2",
"map": "CX.4 / EI-2-4"
},
{
"identity": "rim",
"map": "II.root or Role.id.root"
},
{
"identity": "servd",
"map": "./IdentifierType"
}
]
},
{
"id": "MolecularSequence.identifier.value",
"path": "MolecularSequence.identifier.value",
"short": "The value that is unique",
"definition": "The portion of the identifier typically relevant to the user and which is unique within the context of the system.",
"comment": "If the value is a full URI, then the system SHALL be urn:ietf:rfc:3986. The value's primary purpose is computational mapping. As a result, it may be normalized for comparison purposes (e.g. removing non-significant whitespace, dashes, etc.) A value formatted for human display can be conveyed using the [Rendered Value extension](http://hl7.org/fhir/R4B/extension-rendered-value.html). Identifier.value is to be treated as case sensitive unless knowledge of the Identifier.system allows the processer to be confident that non-case-sensitive processing is safe.",
"min": 0,
"max": "1",
"base": {
"path": "Identifier.value",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"example": [
{
"label": "General",
"valueString": "123456"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "v2",
"map": "CX.1 / EI.1"
},
{
"identity": "rim",
"map": "II.extension or II.root if system indicates OID or GUID (Or Role.id.extension or root)"
},
{
"identity": "servd",
"map": "./Value"
}
]
},
{
"id": "MolecularSequence.identifier.period",
"path": "MolecularSequence.identifier.period",
"short": "Time period when id is/was valid for use",
"definition": "Time period during which identifier is/was valid for use.",
"min": 0,
"max": "1",
"base": {
"path": "Identifier.period",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Period"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "v2",
"map": "CX.7 + CX.8"
},
{
"identity": "rim",
"map": "Role.effectiveTime or implied by context"
},
{
"identity": "servd",
"map": "./StartDate and ./EndDate"
}
]
},
{
"id": "MolecularSequence.identifier.assigner",
"path": "MolecularSequence.identifier.assigner",
"short": "Organization that issued id (may be just text)",
"definition": "Organization that issued/manages the identifier.",
"comment": "The Identifier.assigner may omit the .reference element and only contain a .display element reflecting the name or other textual information about the assigning organization.",
"min": 0,
"max": "1",
"base": {
"path": "Identifier.assigner",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Organization|4.3.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "v2",
"map": "CX.4 / (CX.4,CX.9,CX.10)"
},
{
"identity": "rim",
"map": "II.assigningAuthorityName but note that this is an improper use by the definition of the field. Also Role.scoper"
},
{
"identity": "servd",
"map": "./IdentifierIssuingAuthority"
}
]
},
{
"id": "MolecularSequence.type",
"path": "MolecularSequence.type",
"short": "aa | dna | rna",
"definition": "Amino Acid Sequence/ DNA Sequence / RNA Sequence.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.type",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "sequenceType"
}
],
"strength": "required",
"description": "Type if a sequence -- DNA, RNA, or amino acid sequence.",
"valueSet": "http://hl7.org/fhir/ValueSet/sequence-type|4.3.0"
}
},
{
"id": "MolecularSequence.coordinateSystem",
"path": "MolecularSequence.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": "MolecularSequence.coordinateSystem",
"min": 1,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.patient",
"path": "MolecularSequence.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": "MolecularSequence.patient",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Patient|4.3.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.patient.id",
"path": "MolecularSequence.patient.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.patient.extension",
"path": "MolecularSequence.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"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.patient.extension:patient",
"path": "MolecularSequence.patient.extension",
"sliceName": "patient",
"short": "STU3: patient additional types",
"definition": "STU3: `Sequence.patient` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.patient` is mapped to FHIR R4B element `MolecularSequence.patient` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.patient` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.patient` with unmapped reference targets: Patient.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/StructureDefinition/alternate-reference|5.2.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.patient.reference",
"path": "MolecularSequence.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"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.patient.type",
"path": "MolecularSequence.patient.type",
"short": "Type the reference refers to (e.g. \"Patient\")",
"definition": "The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.\n\nThe type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. \"Patient\" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).",
"comment": "This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.type",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/binding-definition",
"valueString": "Aa resource (or, for logical models, the URI of the logical model)."
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "FHIRResourceTypeExt"
}
],
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/resource-types|4.3.0"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.patient.identifier",
"path": "MolecularSequence.patient.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents 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.\n\nReference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any).",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "MolecularSequence.patient.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "MolecularSequence.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"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.specimen",
"path": "MolecularSequence.specimen",
"short": "Specimen used for sequencing",
"definition": "Specimen used for sequencing.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.specimen",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Specimen|4.3.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.specimen.id",
"path": "MolecularSequence.specimen.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.specimen.extension",
"path": "MolecularSequence.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"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.specimen.extension:specimen",
"path": "MolecularSequence.specimen.extension",
"sliceName": "specimen",
"short": "STU3: specimen additional types",
"definition": "STU3: `Sequence.specimen` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.specimen` is mapped to FHIR R4B element `MolecularSequence.specimen` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.specimen` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.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|5.2.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.specimen.reference",
"path": "MolecularSequence.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"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.specimen.type",
"path": "MolecularSequence.specimen.type",
"short": "Type the reference refers to (e.g. \"Patient\")",
"definition": "The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.\n\nThe type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. \"Patient\" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).",
"comment": "This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.type",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/binding-definition",
"valueString": "Aa resource (or, for logical models, the URI of the logical model)."
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "FHIRResourceTypeExt"
}
],
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/resource-types|4.3.0"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.specimen.identifier",
"path": "MolecularSequence.specimen.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents 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.\n\nReference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any).",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "MolecularSequence.specimen.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "MolecularSequence.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"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.device",
"path": "MolecularSequence.device",
"short": "The method for sequencing",
"definition": "The method for sequencing, for example, chip information.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.device",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Device|4.3.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.device.id",
"path": "MolecularSequence.device.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.device.extension",
"path": "MolecularSequence.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"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.device.extension:device",
"path": "MolecularSequence.device.extension",
"sliceName": "device",
"short": "STU3: device additional types",
"definition": "STU3: `Sequence.device` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.device` is mapped to FHIR R4B element `MolecularSequence.device` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.device` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.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|5.2.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.device.reference",
"path": "MolecularSequence.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"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.device.type",
"path": "MolecularSequence.device.type",
"short": "Type the reference refers to (e.g. \"Patient\")",
"definition": "The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.\n\nThe type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. \"Patient\" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).",
"comment": "This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.type",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/binding-definition",
"valueString": "Aa resource (or, for logical models, the URI of the logical model)."
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "FHIRResourceTypeExt"
}
],
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/resource-types|4.3.0"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.device.identifier",
"path": "MolecularSequence.device.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents 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.\n\nReference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any).",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "MolecularSequence.device.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "MolecularSequence.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"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.performer",
"path": "MolecularSequence.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": "MolecularSequence.performer",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Organization|4.3.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.performer.id",
"path": "MolecularSequence.performer.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.performer.extension",
"path": "MolecularSequence.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"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.performer.extension:performer",
"path": "MolecularSequence.performer.extension",
"sliceName": "performer",
"short": "STU3: performer additional types",
"definition": "STU3: `Sequence.performer` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.performer` is mapped to FHIR R4B element `MolecularSequence.performer` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.performer` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.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|5.2.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.performer.reference",
"path": "MolecularSequence.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"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.performer.type",
"path": "MolecularSequence.performer.type",
"short": "Type the reference refers to (e.g. \"Patient\")",
"definition": "The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.\n\nThe type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. \"Patient\" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).",
"comment": "This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.type",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/binding-definition",
"valueString": "Aa resource (or, for logical models, the URI of the logical model)."
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "FHIRResourceTypeExt"
}
],
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/resource-types|4.3.0"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.performer.identifier",
"path": "MolecularSequence.performer.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents 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.\n\nReference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any).",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "MolecularSequence.performer.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "MolecularSequence.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"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.quantity",
"path": "MolecularSequence.quantity",
"short": "The number of copies of the sequence of interest. (RNASeq)",
"definition": "The number of copies of the sequence of interest. (RNASeq).",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.quantity",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Quantity"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.referenceSeq",
"path": "MolecularSequence.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": "MolecularSequence.referenceSeq",
"min": 0,
"max": "1"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children unless an empty Parameters resource",
"expression": "hasValue() or (children().count() > id.count()) or $this is Parameters",
"xpath": "@value|f:*|h:div|self::f:Parameters",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"key": "msq-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/MolecularSequence|4.3.0"
},
{
"key": "msq-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/MolecularSequence|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.referenceSeq.id",
"path": "MolecularSequence.referenceSeq.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.referenceSeq.extension",
"path": "MolecularSequence.referenceSeq.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. 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 can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.referenceSeq.modifierExtension",
"path": "MolecularSequence.referenceSeq.modifierExtension",
"short": "Extensions that cannot be ignored even if unrecognized",
"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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"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.",
"requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4B/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.referenceSeq.chromosome",
"path": "MolecularSequence.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": "MolecularSequence.referenceSeq.chromosome",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "chromosome-human"
}
],
"strength": "example",
"description": "The chromosome containing the genetic finding",
"valueSet": "http://hl7.org/fhir/ValueSet/chromosome-human|4.3.0"
}
},
{
"id": "MolecularSequence.referenceSeq.genomeBuild",
"path": "MolecularSequence.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": "MolecularSequence.referenceSeq.genomeBuild",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.referenceSeq.orientation",
"path": "MolecularSequence.referenceSeq.orientation",
"short": "sense | antisense",
"definition": "A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the \"sense\" strand, and the opposite complementary strand is the \"antisense\" strand.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.referenceSeq.orientation",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "orientationType"
}
],
"strength": "required",
"description": "Type for orientation",
"valueSet": "http://hl7.org/fhir/ValueSet/orientation-type|4.3.0"
}
},
{
"id": "MolecularSequence.referenceSeq.referenceSeqId",
"path": "MolecularSequence.referenceSeq.referenceSeqId",
"short": "Reference identifier",
"definition": "Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.referenceSeq.referenceSeqId",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "sequenceReference"
}
],
"strength": "example",
"description": "Reference identifier for reference sequence",
"valueSet": "http://hl7.org/fhir/ValueSet/sequence-referenceSeq|4.3.0"
}
},
{
"id": "MolecularSequence.referenceSeq.referenceSeqPointer",
"path": "MolecularSequence.referenceSeq.referenceSeqPointer",
"short": "A pointer to another MolecularSequence entity as reference sequence",
"definition": "A pointer to another MolecularSequence entity as reference sequence.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.referenceSeq.referenceSeqPointer",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.3.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.referenceSeq.referenceSeqPointer.id",
"path": "MolecularSequence.referenceSeq.referenceSeqPointer.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.referenceSeq.referenceSeqPointer.extension",
"path": "MolecularSequence.referenceSeq.referenceSeqPointer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.referenceSeq.referenceSeqPointer.extension:referenceSeqPointer",
"path": "MolecularSequence.referenceSeq.referenceSeqPointer.extension",
"sliceName": "referenceSeqPointer",
"short": "STU3: A Pointer to another Sequence entity as reference sequence additional types",
"definition": "STU3: `Sequence.referenceSeq.referenceSeqPointer` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.referenceSeq.referenceSeqPointer` is mapped to FHIR R4B element `MolecularSequence.referenceSeq.referenceSeqPointer` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.referenceSeq.referenceSeqPointer` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.referenceSeq.referenceSeqPointer` with unmapped reference targets: Sequence.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/StructureDefinition/alternate-reference|5.2.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.referenceSeq.referenceSeqPointer.reference",
"path": "MolecularSequence.referenceSeq.referenceSeqPointer.reference",
"short": "Literal reference, Relative, internal or absolute URL",
"definition": "A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.",
"comment": "Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure \"/[type]/[id]\" then it should be assumed that the reference is to a FHIR RESTful server.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.reference",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"condition": [
"ref-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.referenceSeq.referenceSeqPointer.type",
"path": "MolecularSequence.referenceSeq.referenceSeqPointer.type",
"short": "Type the reference refers to (e.g. \"Patient\")",
"definition": "The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.\n\nThe type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. \"Patient\" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).",
"comment": "This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.type",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/binding-definition",
"valueString": "Aa resource (or, for logical models, the URI of the logical model)."
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "FHIRResourceTypeExt"
}
],
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/resource-types|4.3.0"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.referenceSeq.referenceSeqPointer.identifier",
"path": "MolecularSequence.referenceSeq.referenceSeqPointer.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents 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.\n\nReference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any).",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "MolecularSequence.referenceSeq.referenceSeqPointer.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "MolecularSequence.referenceSeq.referenceSeqPointer.display",
"short": "Text alternative for the resource",
"definition": "Plain text narrative that identifies the resource in addition to the resource reference.",
"comment": "This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.display",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.referenceSeq.referenceSeqString",
"path": "MolecularSequence.referenceSeq.referenceSeqString",
"short": "A string to represent reference sequence",
"definition": "A string like \"ACGT\".",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.referenceSeq.referenceSeqString",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.referenceSeq.strand",
"path": "MolecularSequence.referenceSeq.strand",
"short": "watson | crick",
"definition": "An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.referenceSeq.strand",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "strandType"
}
],
"strength": "required",
"description": "Type for strand",
"valueSet": "http://hl7.org/fhir/ValueSet/strand-type|4.3.0"
}
},
{
"id": "MolecularSequence.referenceSeq.strand.id",
"path": "MolecularSequence.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": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.referenceSeq.strand.extension",
"path": "MolecularSequence.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"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.referenceSeq.strand.extension:strand",
"path": "MolecularSequence.referenceSeq.strand.extension",
"sliceName": "strand",
"short": "STU3: Directionality of DNA ( +1/-1) additional types",
"definition": "STU3: `Sequence.referenceSeq.strand` additional types (integer) additional types from child elements (value)",
"comment": "Element `Sequence.referenceSeq.strand` is mapped to FHIR R4B element `MolecularSequence.referenceSeq.strand` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.referenceSeq.strand` do not cover the following types: integer.\nThe mappings for `Sequence.referenceSeq.strand` do not cover the following types based on type expansion: value.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.referenceSeq.strand|0.1.0"
]
}
],
"condition": [
"ele-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children unless an empty Parameters resource",
"expression": "hasValue() or (children().count() > id.count()) or $this is Parameters",
"xpath": "@value|f:*|h:div|self::f:Parameters",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.referenceSeq.strand.value",
"path": "MolecularSequence.referenceSeq.strand.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-fhir-type",
"valueUrl": "code"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/regex",
"valueString": "[^\\s]+(\\s[^\\s]+)*"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.referenceSeq.windowStart",
"path": "MolecularSequence.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": 0,
"max": "1",
"base": {
"path": "MolecularSequence.referenceSeq.windowStart",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.referenceSeq.windowEnd",
"path": "MolecularSequence.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 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": "MolecularSequence.referenceSeq.windowEnd",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.variant",
"path": "MolecularSequence.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": "MolecularSequence.variant",
"min": 0,
"max": "*"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children unless an empty Parameters resource",
"expression": "hasValue() or (children().count() > id.count()) or $this is Parameters",
"xpath": "@value|f:*|h:div|self::f:Parameters",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.variant.id",
"path": "MolecularSequence.variant.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.variant.extension",
"path": "MolecularSequence.variant.extension",
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. 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 can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.variant.modifierExtension",
"path": "MolecularSequence.variant.modifierExtension",
"short": "Extensions that cannot be ignored even if unrecognized",
"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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"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.",
"requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4B/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.variant.start",
"path": "MolecularSequence.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": "MolecularSequence.variant.start",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.variant.end",
"path": "MolecularSequence.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 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": "MolecularSequence.variant.end",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.variant.observedAllele",
"path": "MolecularSequence.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": "MolecularSequence.variant.observedAllele",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.variant.referenceAllele",
"path": "MolecularSequence.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": "MolecularSequence.variant.referenceAllele",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.variant.cigar",
"path": "MolecularSequence.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": "MolecularSequence.variant.cigar",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.variant.variantPointer",
"path": "MolecularSequence.variant.variantPointer",
"short": "Pointer to observed variant information",
"definition": "A pointer to an Observation containing variant information.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.variant.variantPointer",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Observation|4.3.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.variant.variantPointer.id",
"path": "MolecularSequence.variant.variantPointer.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.variant.variantPointer.extension",
"path": "MolecularSequence.variant.variantPointer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.variant.variantPointer.extension:variantPointer",
"path": "MolecularSequence.variant.variantPointer.extension",
"sliceName": "variantPointer",
"short": "STU3: variantPointer additional types",
"definition": "STU3: `Sequence.variant.variantPointer` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.variant.variantPointer` is mapped to FHIR R4B element `MolecularSequence.variant.variantPointer` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.variant.variantPointer` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.variant.variantPointer` with unmapped reference targets: Observation.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/StructureDefinition/alternate-reference|5.2.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.variant.variantPointer.reference",
"path": "MolecularSequence.variant.variantPointer.reference",
"short": "Literal reference, Relative, internal or absolute URL",
"definition": "A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.",
"comment": "Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure \"/[type]/[id]\" then it should be assumed that the reference is to a FHIR RESTful server.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.reference",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"condition": [
"ref-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.variant.variantPointer.type",
"path": "MolecularSequence.variant.variantPointer.type",
"short": "Type the reference refers to (e.g. \"Patient\")",
"definition": "The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.\n\nThe type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. \"Patient\" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).",
"comment": "This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.type",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/binding-definition",
"valueString": "Aa resource (or, for logical models, the URI of the logical model)."
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "FHIRResourceTypeExt"
}
],
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/resource-types|4.3.0"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.variant.variantPointer.identifier",
"path": "MolecularSequence.variant.variantPointer.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents 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.\n\nReference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any).",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "MolecularSequence.variant.variantPointer.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "MolecularSequence.variant.variantPointer.display",
"short": "Text alternative for the resource",
"definition": "Plain text narrative that identifies the resource in addition to the resource reference.",
"comment": "This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.display",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.observedSeq",
"path": "MolecularSequence.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 start from referenceSeq.windowStart and end by referenceSeq.windowEnd.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.observedSeq",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality",
"path": "MolecularSequence.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": "MolecularSequence.quality",
"min": 0,
"max": "*"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children unless an empty Parameters resource",
"expression": "hasValue() or (children().count() > id.count()) or $this is Parameters",
"xpath": "@value|f:*|h:div|self::f:Parameters",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.id",
"path": "MolecularSequence.quality.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.quality.extension",
"path": "MolecularSequence.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. 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 can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.quality.modifierExtension",
"path": "MolecularSequence.quality.modifierExtension",
"short": "Extensions that cannot be ignored even if unrecognized",
"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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"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.",
"requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4B/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.quality.type",
"path": "MolecularSequence.quality.type",
"short": "indel | snp | unknown",
"definition": "INDEL / SNP / Undefined variant.",
"min": 1,
"max": "1",
"base": {
"path": "MolecularSequence.quality.type",
"min": 1,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "qualityType"
}
],
"strength": "required",
"description": "Type for quality",
"valueSet": "http://hl7.org/fhir/ValueSet/quality-type|4.3.0"
}
},
{
"id": "MolecularSequence.quality.standardSequence",
"path": "MolecularSequence.quality.standardSequence",
"short": "Standard sequence for comparison",
"definition": "Gold standard sequence used for comparing against.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.quality.standardSequence",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "qualityStandardSequence"
}
],
"strength": "example",
"description": "Reference identifier for standard sequence",
"valueSet": "http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence|4.3.0"
}
},
{
"id": "MolecularSequence.quality.start",
"path": "MolecularSequence.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": "MolecularSequence.quality.start",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.end",
"path": "MolecularSequence.quality.end",
"short": "End position of the sequence",
"definition": "End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.quality.end",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.score",
"path": "MolecularSequence.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": "MolecularSequence.quality.score",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Quantity"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.method",
"path": "MolecularSequence.quality.method",
"short": "Method to get quality",
"definition": "Which method is used to get sequence quality.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.quality.method",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "qualityMethod"
}
],
"strength": "example",
"description": "How to get the numerical score",
"valueSet": "http://hl7.org/fhir/ValueSet/sequence-quality-method|4.3.0"
}
},
{
"id": "MolecularSequence.quality.truthTP",
"path": "MolecularSequence.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": "MolecularSequence.quality.truthTP",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.queryTP",
"path": "MolecularSequence.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": "MolecularSequence.quality.queryTP",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.truthFN",
"path": "MolecularSequence.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": "MolecularSequence.quality.truthFN",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.queryFP",
"path": "MolecularSequence.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": "MolecularSequence.quality.queryFP",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.gtFP",
"path": "MolecularSequence.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": "MolecularSequence.quality.gtFP",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.precision",
"path": "MolecularSequence.quality.precision",
"short": "Precision of comparison",
"definition": "QUERY.TP / (QUERY.TP + QUERY.FP).",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.quality.precision",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.recall",
"path": "MolecularSequence.quality.recall",
"short": "Recall of comparison",
"definition": "TRUTH.TP / (TRUTH.TP + TRUTH.FN).",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.quality.recall",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.fScore",
"path": "MolecularSequence.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": "MolecularSequence.quality.fScore",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.roc",
"path": "MolecularSequence.quality.roc",
"short": "Receiver Operator Characteristic (ROC) Curve",
"definition": "Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.quality.roc",
"min": 0,
"max": "1"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children unless an empty Parameters resource",
"expression": "hasValue() or (children().count() > id.count()) or $this is Parameters",
"xpath": "@value|f:*|h:div|self::f:Parameters",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.roc.id",
"path": "MolecularSequence.quality.roc.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.quality.roc.extension",
"path": "MolecularSequence.quality.roc.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. 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 can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.quality.roc.modifierExtension",
"path": "MolecularSequence.quality.roc.modifierExtension",
"short": "Extensions that cannot be ignored even if unrecognized",
"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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"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.",
"requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4B/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.quality.roc.score",
"path": "MolecularSequence.quality.roc.score",
"short": "Genotype quality score",
"definition": "Invidual data point representing the GQ (genotype quality) score threshold.",
"min": 0,
"max": "*",
"base": {
"path": "MolecularSequence.quality.roc.score",
"min": 0,
"max": "*"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.roc.numTP",
"path": "MolecularSequence.quality.roc.numTP",
"short": "Roc score true positive numbers",
"definition": "The number of true positives if the GQ score threshold was set to \"score\" field value.",
"min": 0,
"max": "*",
"base": {
"path": "MolecularSequence.quality.roc.numTP",
"min": 0,
"max": "*"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.roc.numFP",
"path": "MolecularSequence.quality.roc.numFP",
"short": "Roc score false positive numbers",
"definition": "The number of false positives if the GQ score threshold was set to \"score\" field value.",
"min": 0,
"max": "*",
"base": {
"path": "MolecularSequence.quality.roc.numFP",
"min": 0,
"max": "*"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.roc.numFN",
"path": "MolecularSequence.quality.roc.numFN",
"short": "Roc score false negative numbers",
"definition": "The number of false negatives if the GQ score threshold was set to \"score\" field value.",
"min": 0,
"max": "*",
"base": {
"path": "MolecularSequence.quality.roc.numFN",
"min": 0,
"max": "*"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.roc.precision",
"path": "MolecularSequence.quality.roc.precision",
"short": "Precision of the GQ score",
"definition": "Calculated precision if the GQ score threshold was set to \"score\" field value.",
"min": 0,
"max": "*",
"base": {
"path": "MolecularSequence.quality.roc.precision",
"min": 0,
"max": "*"
},
"type": [
{
"code": "decimal"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.roc.sensitivity",
"path": "MolecularSequence.quality.roc.sensitivity",
"short": "Sensitivity of the GQ score",
"definition": "Calculated sensitivity if the GQ score threshold was set to \"score\" field value.",
"min": 0,
"max": "*",
"base": {
"path": "MolecularSequence.quality.roc.sensitivity",
"min": 0,
"max": "*"
},
"type": [
{
"code": "decimal"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.quality.roc.fMeasure",
"path": "MolecularSequence.quality.roc.fMeasure",
"short": "FScore of the GQ score",
"definition": "Calculated fScore if the GQ score threshold was set to \"score\" field value.",
"min": 0,
"max": "*",
"base": {
"path": "MolecularSequence.quality.roc.fMeasure",
"min": 0,
"max": "*"
},
"type": [
{
"code": "decimal"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.readCoverage",
"path": "MolecularSequence.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": "MolecularSequence.readCoverage",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.repository",
"path": "MolecularSequence.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": "MolecularSequence.repository",
"min": 0,
"max": "*"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children unless an empty Parameters resource",
"expression": "hasValue() or (children().count() > id.count()) or $this is Parameters",
"xpath": "@value|f:*|h:div|self::f:Parameters",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.repository.id",
"path": "MolecularSequence.repository.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.repository.extension",
"path": "MolecularSequence.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. 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 can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.repository.modifierExtension",
"path": "MolecularSequence.repository.modifierExtension",
"short": "Extensions that cannot be ignored even if unrecognized",
"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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"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.",
"requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4B/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.repository.type",
"path": "MolecularSequence.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": "MolecularSequence.repository.type",
"min": 1,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "repositoryType"
}
],
"strength": "required",
"description": "Type for repository",
"valueSet": "http://hl7.org/fhir/ValueSet/repository-type|4.3.0"
}
},
{
"id": "MolecularSequence.repository.url",
"path": "MolecularSequence.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": "MolecularSequence.repository.url",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.repository.name",
"path": "MolecularSequence.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": "MolecularSequence.repository.name",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.repository.datasetId",
"path": "MolecularSequence.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": "MolecularSequence.repository.datasetId",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.repository.variantsetId",
"path": "MolecularSequence.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": "MolecularSequence.repository.variantsetId",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.repository.readsetId",
"path": "MolecularSequence.repository.readsetId",
"short": "Id of the read",
"definition": "Id of the read in this external repository.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.repository.readsetId",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.pointer",
"path": "MolecularSequence.pointer",
"short": "Pointer to next atomic sequence",
"definition": "Pointer to next atomic sequence which at most contains one variant.",
"min": 0,
"max": "*",
"base": {
"path": "MolecularSequence.pointer",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.3.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.pointer.id",
"path": "MolecularSequence.pointer.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.pointer.extension",
"path": "MolecularSequence.pointer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"ordered": false,
"rules": "open"
},
"short": "Extension",
"definition": "An Extension",
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.pointer.extension:pointer",
"path": "MolecularSequence.pointer.extension",
"sliceName": "pointer",
"short": "STU3: pointer additional types",
"definition": "STU3: `Sequence.pointer` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.pointer` is mapped to FHIR R4B element `MolecularSequence.pointer` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.pointer` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.pointer` with unmapped reference targets: Sequence.",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/StructureDefinition/alternate-reference|5.2.0"
]
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "MolecularSequence.pointer.reference",
"path": "MolecularSequence.pointer.reference",
"short": "Literal reference, Relative, internal or absolute URL",
"definition": "A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.",
"comment": "Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure \"/[type]/[id]\" then it should be assumed that the reference is to a FHIR RESTful server.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.reference",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"condition": [
"ref-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.pointer.type",
"path": "MolecularSequence.pointer.type",
"short": "Type the reference refers to (e.g. \"Patient\")",
"definition": "The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.\n\nThe type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. \"Patient\" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).",
"comment": "This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.type",
"min": 0,
"max": "1"
},
"type": [
{
"code": "uri"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/build/StructureDefinition/binding-definition",
"valueString": "Aa resource (or, for logical models, the URI of the logical model)."
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "FHIRResourceTypeExt"
}
],
"strength": "extensible",
"valueSet": "http://hl7.org/fhir/ValueSet/resource-types|4.3.0"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.pointer.identifier",
"path": "MolecularSequence.pointer.identifier",
"short": "Logical reference, when literal reference is not known",
"definition": "An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents 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.\n\nReference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any).",
"min": 0,
"max": "1",
"base": {
"path": "Reference.identifier",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Identifier"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": ".identifier"
}
]
},
{
"id": "MolecularSequence.pointer.display",
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
},
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
"valueBoolean": true
}
],
"path": "MolecularSequence.pointer.display",
"short": "Text alternative for the resource",
"definition": "Plain text narrative that identifies the resource in addition to the resource reference.",
"comment": "This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.",
"min": 0,
"max": "1",
"base": {
"path": "Reference.display",
"min": 0,
"max": "1"
},
"type": [
{
"code": "string"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"isModifier": false,
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.structureVariant",
"path": "MolecularSequence.structureVariant",
"short": "Structural variant",
"definition": "Information about chromosome structure variation.",
"min": 0,
"max": "*",
"base": {
"path": "MolecularSequence.structureVariant",
"min": 0,
"max": "*"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children unless an empty Parameters resource",
"expression": "hasValue() or (children().count() > id.count()) or $this is Parameters",
"xpath": "@value|f:*|h:div|self::f:Parameters",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.structureVariant.id",
"path": "MolecularSequence.structureVariant.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.structureVariant.extension",
"path": "MolecularSequence.structureVariant.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. 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 can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.structureVariant.modifierExtension",
"path": "MolecularSequence.structureVariant.modifierExtension",
"short": "Extensions that cannot be ignored even if unrecognized",
"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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"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.",
"requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4B/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.structureVariant.variantType",
"path": "MolecularSequence.structureVariant.variantType",
"short": "Structural variant change type",
"definition": "Information about chromosome structure variation DNA change type.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.structureVariant.variantType",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true,
"binding": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "LOINC LL379-9 answerlist"
}
],
"strength": "required",
"description": "DNA change type.",
"valueSet": "http://loinc.org/vs/LL379-9|4.3.0"
}
},
{
"id": "MolecularSequence.structureVariant.exact",
"path": "MolecularSequence.structureVariant.exact",
"short": "Does the structural variant have base pair resolution breakpoints?",
"definition": "Used to indicate if the outer and inner start-end values have the same meaning.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.structureVariant.exact",
"min": 0,
"max": "1"
},
"type": [
{
"code": "boolean"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.structureVariant.length",
"path": "MolecularSequence.structureVariant.length",
"short": "Structural variant length",
"definition": "Length of the variant chromosome.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.structureVariant.length",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.structureVariant.outer",
"path": "MolecularSequence.structureVariant.outer",
"short": "Structural variant outer",
"definition": "Structural variant outer.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.structureVariant.outer",
"min": 0,
"max": "1"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children unless an empty Parameters resource",
"expression": "hasValue() or (children().count() > id.count()) or $this is Parameters",
"xpath": "@value|f:*|h:div|self::f:Parameters",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.structureVariant.outer.id",
"path": "MolecularSequence.structureVariant.outer.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.structureVariant.outer.extension",
"path": "MolecularSequence.structureVariant.outer.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. 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 can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.structureVariant.outer.modifierExtension",
"path": "MolecularSequence.structureVariant.outer.modifierExtension",
"short": "Extensions that cannot be ignored even if unrecognized",
"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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"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.",
"requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4B/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.structureVariant.outer.start",
"path": "MolecularSequence.structureVariant.outer.start",
"short": "Structural variant outer start",
"definition": "Structural variant outer start. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.structureVariant.outer.start",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.structureVariant.outer.end",
"path": "MolecularSequence.structureVariant.outer.end",
"short": "Structural variant outer end",
"definition": "Structural variant outer end. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.structureVariant.outer.end",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.structureVariant.inner",
"path": "MolecularSequence.structureVariant.inner",
"short": "Structural variant inner",
"definition": "Structural variant inner.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.structureVariant.inner",
"min": 0,
"max": "1"
},
"type": [
{
"code": "BackboneElement"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children unless an empty Parameters resource",
"expression": "hasValue() or (children().count() > id.count()) or $this is Parameters",
"xpath": "@value|f:*|h:div|self::f:Parameters",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.structureVariant.inner.id",
"path": "MolecularSequence.structureVariant.inner.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "string"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.structureVariant.inner.extension",
"path": "MolecularSequence.structureVariant.inner.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. 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 can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "MolecularSequence.structureVariant.inner.modifierExtension",
"path": "MolecularSequence.structureVariant.inner.modifierExtension",
"short": "Extensions that cannot be ignored even if unrecognized",
"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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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.\n\nModifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).",
"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.",
"requirements": "Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4B/extensibility.html#modifierExtension).",
"alias": [
"extensions",
"user content",
"modifiers"
],
"min": 0,
"max": "*",
"base": {
"path": "BackboneElement.modifierExtension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
},
{
"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|4.3.0"
}
],
"isModifier": true,
"isModifierReason": "Modifier extensions are expected to modify the meaning or interpretation of the element that contains them",
"isSummary": true,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "MolecularSequence.structureVariant.inner.start",
"path": "MolecularSequence.structureVariant.inner.start",
"short": "Structural variant inner start",
"definition": "Structural variant inner start. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.structureVariant.inner.start",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
},
{
"id": "MolecularSequence.structureVariant.inner.end",
"path": "MolecularSequence.structureVariant.inner.end",
"short": "Structural variant inner end",
"definition": "Structural variant inner end. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"min": 0,
"max": "1",
"base": {
"path": "MolecularSequence.structureVariant.inner.end",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element|4.3.0"
}
],
"mustSupport": false,
"isModifier": false,
"isSummary": true
}
]
},
"differential": {
"element": [
{
"id": "MolecularSequence",
"path": "MolecularSequence"
},
{
"id": "MolecularSequence.meta.extension",
"path": "MolecularSequence.meta.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "MolecularSequence.meta.extension:meta",
"path": "MolecularSequence.meta.extension",
"sliceName": "meta",
"short": "STU3: meta additional types",
"definition": "STU3: `Sequence.meta` additional types (Meta) additional types from child elements (lastUpdated, profile, security, tag, versionId)",
"comment": "Element `Sequence.meta` is mapped to FHIR R4B element `MolecularSequence.meta` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.meta` do not cover the following types: Meta.\nThe mappings for `Sequence.meta` do not cover the following types based on type expansion: lastUpdated, profile, security, tag, versionId.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.meta|0.1.0"
]
}
]
},
{
"id": "MolecularSequence.text.extension",
"path": "MolecularSequence.text.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "MolecularSequence.text.extension:text",
"path": "MolecularSequence.text.extension",
"sliceName": "text",
"short": "STU3: text additional types",
"definition": "STU3: `Sequence.text` additional types (Narrative) additional types from child elements (div, status)",
"comment": "Element `Sequence.text` is mapped to FHIR R4B element `MolecularSequence.text` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.text` do not cover the following types: Narrative.\nThe mappings for `Sequence.text` do not cover the following types based on type expansion: div, status.\nContained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a \"text blob\" or where text is additionally entered raw or narrated and encoded in formation is added later.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.text|0.1.0"
]
}
]
},
{
"id": "MolecularSequence.identifier.extension",
"path": "MolecularSequence.identifier.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "MolecularSequence.identifier.extension:identifier",
"path": "MolecularSequence.identifier.extension",
"sliceName": "identifier",
"short": "STU3: identifier additional types",
"definition": "STU3: `Sequence.identifier` additional types (Identifier) additional types from child elements (assigner, period, system, type, use, value)",
"comment": "Element `Sequence.identifier` is mapped to FHIR R4B element `MolecularSequence.identifier` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.identifier` do not cover the following types: Identifier.\nThe mappings for `Sequence.identifier` do not cover the following types based on type expansion: assigner, period, system, type, use, value.",
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.identifier|0.1.0"
]
}
]
},
{
"id": "MolecularSequence.patient.extension",
"path": "MolecularSequence.patient.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "MolecularSequence.patient.extension:patient",
"path": "MolecularSequence.patient.extension",
"sliceName": "patient",
"short": "STU3: patient additional types",
"definition": "STU3: `Sequence.patient` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.patient` is mapped to FHIR R4B element `MolecularSequence.patient` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.patient` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.patient` with unmapped reference targets: Patient.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/StructureDefinition/alternate-reference|5.2.0"
]
}
]
},
{
"id": "MolecularSequence.specimen.extension",
"path": "MolecularSequence.specimen.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "MolecularSequence.specimen.extension:specimen",
"path": "MolecularSequence.specimen.extension",
"sliceName": "specimen",
"short": "STU3: specimen additional types",
"definition": "STU3: `Sequence.specimen` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.specimen` is mapped to FHIR R4B element `MolecularSequence.specimen` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.specimen` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.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|5.2.0"
]
}
]
},
{
"id": "MolecularSequence.device.extension",
"path": "MolecularSequence.device.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "MolecularSequence.device.extension:device",
"path": "MolecularSequence.device.extension",
"sliceName": "device",
"short": "STU3: device additional types",
"definition": "STU3: `Sequence.device` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.device` is mapped to FHIR R4B element `MolecularSequence.device` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.device` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.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|5.2.0"
]
}
]
},
{
"id": "MolecularSequence.performer.extension",
"path": "MolecularSequence.performer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "MolecularSequence.performer.extension:performer",
"path": "MolecularSequence.performer.extension",
"sliceName": "performer",
"short": "STU3: performer additional types",
"definition": "STU3: `Sequence.performer` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.performer` is mapped to FHIR R4B element `MolecularSequence.performer` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.performer` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.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|5.2.0"
]
}
]
},
{
"id": "MolecularSequence.referenceSeq.referenceSeqPointer.extension",
"path": "MolecularSequence.referenceSeq.referenceSeqPointer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "MolecularSequence.referenceSeq.referenceSeqPointer.extension:referenceSeqPointer",
"path": "MolecularSequence.referenceSeq.referenceSeqPointer.extension",
"sliceName": "referenceSeqPointer",
"short": "STU3: A Pointer to another Sequence entity as reference sequence additional types",
"definition": "STU3: `Sequence.referenceSeq.referenceSeqPointer` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.referenceSeq.referenceSeqPointer` is mapped to FHIR R4B element `MolecularSequence.referenceSeq.referenceSeqPointer` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.referenceSeq.referenceSeqPointer` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.referenceSeq.referenceSeqPointer` with unmapped reference targets: Sequence.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/StructureDefinition/alternate-reference|5.2.0"
]
}
]
},
{
"id": "MolecularSequence.referenceSeq.strand.extension",
"path": "MolecularSequence.referenceSeq.strand.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "MolecularSequence.referenceSeq.strand.extension:strand",
"path": "MolecularSequence.referenceSeq.strand.extension",
"sliceName": "strand",
"short": "STU3: Directionality of DNA ( +1/-1) additional types",
"definition": "STU3: `Sequence.referenceSeq.strand` additional types (integer) additional types from child elements (value)",
"comment": "Element `Sequence.referenceSeq.strand` is mapped to FHIR R4B element `MolecularSequence.referenceSeq.strand` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.referenceSeq.strand` do not cover the following types: integer.\nThe mappings for `Sequence.referenceSeq.strand` do not cover the following types based on type expansion: value.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.referenceSeq.strand|0.1.0"
]
}
]
},
{
"id": "MolecularSequence.variant.variantPointer.extension",
"path": "MolecularSequence.variant.variantPointer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "MolecularSequence.variant.variantPointer.extension:variantPointer",
"path": "MolecularSequence.variant.variantPointer.extension",
"sliceName": "variantPointer",
"short": "STU3: variantPointer additional types",
"definition": "STU3: `Sequence.variant.variantPointer` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.variant.variantPointer` is mapped to FHIR R4B element `MolecularSequence.variant.variantPointer` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.variant.variantPointer` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.variant.variantPointer` with unmapped reference targets: Observation.",
"min": 0,
"max": "1",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/StructureDefinition/alternate-reference|5.2.0"
]
}
]
},
{
"id": "MolecularSequence.pointer.extension",
"path": "MolecularSequence.pointer.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 0,
"max": "*"
},
{
"id": "MolecularSequence.pointer.extension:pointer",
"path": "MolecularSequence.pointer.extension",
"sliceName": "pointer",
"short": "STU3: pointer additional types",
"definition": "STU3: `Sequence.pointer` additional types from child elements (display, identifier, reference)",
"comment": "Element `Sequence.pointer` is mapped to FHIR R4B element `MolecularSequence.pointer` as `SourceIsBroaderThanTarget`.\nThe mappings for `Sequence.pointer` do not cover the following types based on type expansion: display, identifier, reference.\nThe standard extension `alternate-reference` has been mapped as the representation of FHIR STU3 element `Sequence.pointer` with unmapped reference targets: Sequence.",
"min": 0,
"max": "*",
"base": {
"path": "DomainResource.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension",
"profile": [
"http://hl7.org/fhir/StructureDefinition/alternate-reference|5.2.0"
]
}
]
}
]
}
}