FHIR IG analytics| Package | hl7.fhir.uv.xver-r3.r5 |
| Resource Type | StructureDefinition |
| Id | StructureDefinition-ext-R3-Sequence.quality.json |
| FHIR Version | R5 |
| Source | http://hl7.org/fhir/uv/xver-r3.r5/0.1.0/StructureDefinition-ext-R3-Sequence.quality.html |
| URL | http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.quality |
| Version | 0.1.0 |
| Status | active |
| Date | 2026-03-17T21:02:03.8104715+00:00 |
| Name | ExtensionSequence_Quality |
| Title | STU3: An set of value as quality of sequence (new) |
| Realm | uv |
| Authority | hl7 |
| Description | STU3: `Sequence.quality` (new:BackboneElement) |
| Purpose | This extension is part of the cross-version definitions generated to enable use of the element `Sequence.quality` as defined in FHIR STU3 in FHIR R5. The source element is defined as: `Sequence.quality` 0..* `BackboneElement` Across FHIR versions, the element set has been mapped as: * STU3: `Sequence.quality` 0..* `BackboneElement` * R4: `MolecularSequence.quality` 0..* `BackboneElement` * R4B: `MolecularSequence.quality` 0..* `BackboneElement` Following are the generation technical comments: Element `Sequence.quality` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`. Element `Sequence.quality` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element). |
| Type | Extension |
| Kind | complex-type |
| ConceptMap | ||
| hl7.fhir.uv.xver-r3.r5#0.1.0 | R3-Sequence-element-map-to-R5 | Cross-version mapping for FHIR STU3 Sequence to FHIR R5 MolecularSequence |
| ValueSet | ||
| hl7.fhir.uv.xver-r3.r5#0.1.0 | R3-quality-type-for-R5 | Cross-version ValueSet STU3.qualityType for use in FHIR R5 |
No extension usage examples found
Note: links and images are rebased to the (stated) source
Generated Narrative: StructureDefinition ext-R3-Sequence.quality
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Extension | 0..* | Extension(5.0.0) | STU3: An set of value as quality of sequence (new) | |
  Slices for extension | 1..* | Extension | Extension Slice: Unordered, Open by value:url | |
   extension:type | 1..1 | Extension | STU3: indel | snp | unknown (new) | |
  url | 1..1 | uri | "type" | |
  value[x] | 1..1 | code | indel | snp | unknown Binding: R3QualityTypeForR5 (0.1.0) (required): Type for quality report | |
| extension:standardSequence | 0..1 | Extension | STU3: Standard sequence for comparison (new) | |
| url | 1..1 | uri | "standardSequence" | |
 value[x] | 0..1 | CodeableConcept | Standard sequence for comparison | |
| extension:start | 0..1 | Extension | STU3: Start position of the sequence (new) | |
| url | 1..1 | uri | "start" | |
| value[x] | 0..1 | integer | Start position of the sequence | |
| extension:end | 0..1 | Extension | STU3: End position of the sequence (new) | |
| url | 1..1 | uri | "end" | |
| value[x] | 0..1 | integer | End position of the sequence | |
| extension:score | 0..1 | Extension | STU3: Quality score for the comparison (new) | |
| url | 1..1 | uri | "score" | |
| value[x] | 0..1 | Quantity | Quality score for the comparison | |
| extension:method | 0..1 | Extension | STU3: Method to get quality (new) | |
| url | 1..1 | uri | "method" | |
| value[x] | 0..1 | CodeableConcept | Method to get quality | |
| extension:truthTP | 0..1 | Extension | STU3: True positives from the perspective of the truth data (new) | |
| url | 1..1 | uri | "truthTP" | |
| value[x] | 0..1 | decimal | True positives from the perspective of the truth data | |
| extension:queryTP | 0..1 | Extension | STU3: True positives from the perspective of the query data (new) | |
| url | 1..1 | uri | "queryTP" | |
| value[x] | 0..1 | decimal | True positives from the perspective of the query data | |
| extension:truthFN | 0..1 | Extension | STU3: False negatives (new) | |
| url | 1..1 | uri | "truthFN" | |
| value[x] | 0..1 | decimal | False negatives | |
| extension:queryFP | 0..1 | Extension | STU3: False positives (new) | |
| url | 1..1 | uri | "queryFP" | |
| value[x] | 0..1 | decimal | False positives | |
| extension:gtFP | 0..1 | Extension | STU3: False positives where the non-REF alleles in the Truth and Query Call Sets match (new) | |
| url | 1..1 | uri | "gtFP" | |
| value[x] | 0..1 | decimal | False positives where the non-REF alleles in the Truth and Query Call Sets match | |
| extension:precision | 0..1 | Extension | STU3: Precision of comparison (new) | |
| url | 1..1 | uri | "precision" | |
| value[x] | 0..1 | decimal | Precision of comparison | |
| extension:recall | 0..1 | Extension | STU3: Recall of comparison (new) | |
| url | 1..1 | uri | "recall" | |
| value[x] | 0..1 | decimal | Recall of comparison | |
 extension:fScore | 0..1 | Extension | STU3: F-score (new) | |
 url | 1..1 | uri | "fScore" | |
| value[x] | 0..1 | decimal | F-score | |
| url | 1..1 | uri | "http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.quality" | |
 value[x] | 0..0 | Value of extension | ||
| Documentation for this format | ||||
FHIR
FHIRsmith{
"resourceType": "StructureDefinition",
"id": "ext-R3-Sequence.quality",
"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.r5"
},
{
"url": "version",
"valueString": "0.1.0"
},
{
"url": "uri",
"valueUri": "http://hl7.org/fhir/uv/xver/ImplementationGuide/hl7.fhir.uv.xver-r3.r5"
}
],
"url": "http://hl7.org/fhir/StructureDefinition/package-source"
},
{
"extension": [
{
"url": "startFhirVersion",
"valueCode": "5.0"
},
{
"url": "endFhirVersion",
"valueCode": "5.0"
}
],
"url": "http://hl7.org/fhir/StructureDefinition/version-specific-use"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-type-characteristics",
"valueCode": "can-bind"
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
"valueInteger": 0,
"_valueInteger": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
"valueCanonical": "http://hl7.org/fhir/uv/xver/ImplementationGuide/hl7.fhir.uv.xver-r3.r5"
}
]
}
},
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
"valueCode": "trial-use",
"_valueCode": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
"valueCanonical": "http://hl7.org/fhir/uv/xver/ImplementationGuide/hl7.fhir.uv.xver-r3.r5"
}
]
}
}
],
"url": "http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.quality",
"version": "0.1.0",
"name": "ExtensionSequence_Quality",
"title": "STU3: An set of value as quality of sequence (new)",
"status": "active",
"experimental": false,
"date": "2026-03-17T21:02:03.8104715+00:00",
"publisher": "FHIR Infrastructure",
"contact": [
{
"name": "FHIR Infrastructure",
"telecom": [
{
"system": "url",
"value": "http://www.hl7.org/Special/committees/fiwg"
}
]
}
],
"description": "STU3: `Sequence.quality` (new:BackboneElement)",
"jurisdiction": [
{
"coding": [
{
"system": "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code": "001",
"display": "World"
}
]
}
],
"purpose": "This extension is part of the cross-version definitions generated to enable use of the\r\nelement `Sequence.quality` as defined in FHIR STU3\r\nin FHIR R5.\r\n\r\nThe source element is defined as:\r\n`Sequence.quality` 0..* `BackboneElement`\r\n\r\nAcross FHIR versions, the element set has been mapped as:\r\n* STU3: `Sequence.quality` 0..* `BackboneElement`\n* R4: `MolecularSequence.quality` 0..* `BackboneElement`\n* R4B: `MolecularSequence.quality` 0..* `BackboneElement`\r\n\r\nFollowing are the generation technical comments:\r\nElement `Sequence.quality` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"fhirVersion": "5.0.0",
"mapping": [
{
"identity": "rim",
"uri": "http://hl7.org/v3",
"name": "RIM Mapping"
}
],
"kind": "complex-type",
"abstract": false,
"context": [
{
"type": "element",
"expression": "MolecularSequence"
}
],
"type": "Extension",
"baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"derivation": "constraint",
"snapshot": {
"extension": [
{
"url": "http://hl7.org/fhir/tools/StructureDefinition/snapshot-base-version",
"valueString": "5.0.0"
}
],
"element": [
{
"id": "Extension",
"path": "Extension",
"short": "STU3: An set of value as quality of sequence (new)",
"definition": "STU3: `Sequence.quality` (new:BackboneElement)",
"comment": "Element `Sequence.quality` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "*",
"base": {
"path": "Extension",
"min": 0,
"max": "*"
},
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false
},
{
"id": "Extension.id",
"path": "Extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension",
"path": "Extension.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": 1,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:type",
"path": "Extension.extension",
"sliceName": "type",
"short": "STU3: indel | snp | unknown (new)",
"definition": "STU3: `Sequence.quality.type` (new:code)",
"comment": "Element `Sequence.quality.type` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.type` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.type` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.type` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.type` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.type` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 1,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:type.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:type.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:type.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "type",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:type.value[x]",
"path": "Extension.extension.value[x]",
"short": "indel | snp | unknown",
"definition": "INDEL / SNP / Undefined variant.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"binding": {
"strength": "required",
"description": "Type for quality report",
"valueSet": "http://hl7.org/fhir/uv/xver/ValueSet/R3-quality-type-for-R5|0.1.0"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:standardSequence",
"path": "Extension.extension",
"sliceName": "standardSequence",
"short": "STU3: Standard sequence for comparison (new)",
"definition": "STU3: `Sequence.quality.standardSequence` (new:CodeableConcept)",
"comment": "Element `Sequence.quality.standardSequence` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.standardSequence` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.standardSequence` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.standardSequence` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.standardSequence` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.standardSequence` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:standardSequence.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:standardSequence.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:standardSequence.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "standardSequence",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:standardSequence.value[x]",
"path": "Extension.extension.value[x]",
"short": "Standard sequence for comparison",
"definition": "Gold standard sequence used for comparing against.",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:start",
"path": "Extension.extension",
"sliceName": "start",
"short": "STU3: Start position of the sequence (new)",
"definition": "STU3: `Sequence.quality.start` (new:integer)",
"comment": "Element `Sequence.quality.start` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.start` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.start` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.start` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.start` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.start` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:start.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:start.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:start.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "start",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:start.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:end",
"path": "Extension.extension",
"sliceName": "end",
"short": "STU3: End position of the sequence (new)",
"definition": "STU3: `Sequence.quality.end` (new:integer)",
"comment": "Element `Sequence.quality.end` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.end` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.end` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.end` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.end` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.end` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:end.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:end.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:end.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "end",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:end.value[x]",
"path": "Extension.extension.value[x]",
"short": "End position of the sequence",
"definition": "End position of the sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:score",
"path": "Extension.extension",
"sliceName": "score",
"short": "STU3: Quality score for the comparison (new)",
"definition": "STU3: `Sequence.quality.score` (new:Quantity)",
"comment": "Element `Sequence.quality.score` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.score` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.score` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.score` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.score` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.score` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:score.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:score.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:score.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "score",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:score.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Quantity"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:method",
"path": "Extension.extension",
"sliceName": "method",
"short": "STU3: Method to get quality (new)",
"definition": "STU3: `Sequence.quality.method` (new:CodeableConcept)",
"comment": "Element `Sequence.quality.method` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.method` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.method` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.method` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.method` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.method` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:method.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:method.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:method.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "method",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:method.value[x]",
"path": "Extension.extension.value[x]",
"short": "Method to get quality",
"definition": "Which method is used to get sequence quality.",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:truthTP",
"path": "Extension.extension",
"sliceName": "truthTP",
"short": "STU3: True positives from the perspective of the truth data (new)",
"definition": "STU3: `Sequence.quality.truthTP` (new:decimal)",
"comment": "Element `Sequence.quality.truthTP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.truthTP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.truthTP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.truthTP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.truthTP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.truthTP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:truthTP.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:truthTP.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:truthTP.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "truthTP",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:truthTP.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:queryTP",
"path": "Extension.extension",
"sliceName": "queryTP",
"short": "STU3: True positives from the perspective of the query data (new)",
"definition": "STU3: `Sequence.quality.queryTP` (new:decimal)",
"comment": "Element `Sequence.quality.queryTP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.queryTP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.queryTP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.queryTP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.queryTP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.queryTP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:queryTP.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:queryTP.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:queryTP.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "queryTP",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:queryTP.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:truthFN",
"path": "Extension.extension",
"sliceName": "truthFN",
"short": "STU3: False negatives (new)",
"definition": "STU3: `Sequence.quality.truthFN` (new:decimal)",
"comment": "Element `Sequence.quality.truthFN` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.truthFN` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.truthFN` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.truthFN` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.truthFN` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.truthFN` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:truthFN.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:truthFN.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:truthFN.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "truthFN",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:truthFN.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:queryFP",
"path": "Extension.extension",
"sliceName": "queryFP",
"short": "STU3: False positives (new)",
"definition": "STU3: `Sequence.quality.queryFP` (new:decimal)",
"comment": "Element `Sequence.quality.queryFP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.queryFP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.queryFP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.queryFP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.queryFP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.queryFP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:queryFP.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:queryFP.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:queryFP.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "queryFP",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:queryFP.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:gtFP",
"path": "Extension.extension",
"sliceName": "gtFP",
"short": "STU3: False positives where the non-REF alleles in the Truth and Query Call Sets match (new)",
"definition": "STU3: `Sequence.quality.gtFP` (new:decimal)",
"comment": "Element `Sequence.quality.gtFP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.gtFP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.gtFP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.gtFP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.gtFP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.gtFP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:gtFP.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:gtFP.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:gtFP.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "gtFP",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:gtFP.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:precision",
"path": "Extension.extension",
"sliceName": "precision",
"short": "STU3: Precision of comparison (new)",
"definition": "STU3: `Sequence.quality.precision` (new:decimal)",
"comment": "Element `Sequence.quality.precision` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.precision` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.precision` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.precision` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.precision` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.precision` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:precision.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:precision.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:precision.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "precision",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:precision.value[x]",
"path": "Extension.extension.value[x]",
"short": "Precision of comparison",
"definition": "QUERY.TP / (QUERY.TP + QUERY.FP).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:recall",
"path": "Extension.extension",
"sliceName": "recall",
"short": "STU3: Recall of comparison (new)",
"definition": "STU3: `Sequence.quality.recall` (new:decimal)",
"comment": "Element `Sequence.quality.recall` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.recall` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.recall` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.recall` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.recall` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.recall` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:recall.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:recall.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:recall.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "recall",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:recall.value[x]",
"path": "Extension.extension.value[x]",
"short": "Recall of comparison",
"definition": "TRUTH.TP / (TRUTH.TP + TRUTH.FN).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:fScore",
"path": "Extension.extension",
"sliceName": "fScore",
"short": "STU3: F-score (new)",
"definition": "STU3: `Sequence.quality.fScore` (new:decimal)",
"comment": "Element `Sequence.quality.fScore` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.fScore` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.fScore` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.fScore` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.fScore` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.fScore` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:fScore.id",
"path": "Extension.extension.id",
"representation": [
"xmlAttr"
],
"short": "Unique id for inter-element referencing",
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min": 0,
"max": "1",
"base": {
"path": "Element.id",
"min": 0,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"condition": [
"ele-1"
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:fScore.extension",
"path": "Extension.extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"description": "Extensions are always sliced by (at least) url",
"rules": "open"
},
"short": "Additional content defined by implementations",
"definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias": [
"extensions",
"user content"
],
"min": 0,
"max": "*",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "n/a"
}
]
},
{
"id": "Extension.extension:fScore.url",
"path": "Extension.extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "fScore",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:fScore.value[x]",
"path": "Extension.extension.value[x]",
"short": "F-score",
"definition": "Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.url",
"path": "Extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.quality",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.value[x]",
"path": "Extension.value[x]",
"short": "Value of extension",
"definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R5/extensibility.html) for a list).",
"min": 0,
"max": "0",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "base64Binary"
},
{
"code": "boolean"
},
{
"code": "canonical"
},
{
"code": "code"
},
{
"code": "date"
},
{
"code": "dateTime"
},
{
"code": "decimal"
},
{
"code": "id"
},
{
"code": "instant"
},
{
"code": "integer"
},
{
"code": "integer64"
},
{
"code": "markdown"
},
{
"code": "oid"
},
{
"code": "positiveInt"
},
{
"code": "string"
},
{
"code": "time"
},
{
"code": "unsignedInt"
},
{
"code": "uri"
},
{
"code": "url"
},
{
"code": "uuid"
},
{
"code": "Address"
},
{
"code": "Age"
},
{
"code": "Annotation"
},
{
"code": "Attachment"
},
{
"code": "CodeableConcept"
},
{
"code": "CodeableReference"
},
{
"code": "Coding"
},
{
"code": "ContactPoint"
},
{
"code": "Count"
},
{
"code": "Distance"
},
{
"code": "Duration"
},
{
"code": "HumanName"
},
{
"code": "Identifier"
},
{
"code": "Money"
},
{
"code": "Period"
},
{
"code": "Quantity"
},
{
"code": "Range"
},
{
"code": "Ratio"
},
{
"code": "RatioRange"
},
{
"code": "Reference"
},
{
"code": "SampledData"
},
{
"code": "Signature"
},
{
"code": "Timing"
},
{
"code": "ContactDetail"
},
{
"code": "DataRequirement"
},
{
"code": "Expression"
},
{
"code": "ParameterDefinition"
},
{
"code": "RelatedArtifact"
},
{
"code": "TriggerDefinition"
},
{
"code": "UsageContext"
},
{
"code": "Availability"
},
{
"code": "ExtendedContactDetail"
},
{
"code": "Dosage"
},
{
"code": "Meta"
}
],
"condition": [
"ext-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
}
]
},
"differential": {
"element": [
{
"id": "Extension",
"path": "Extension",
"short": "STU3: An set of value as quality of sequence (new)",
"definition": "STU3: `Sequence.quality` (new:BackboneElement)",
"comment": "Element `Sequence.quality` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "*",
"base": {
"path": "Extension",
"min": 0,
"max": "*"
},
"isModifier": false
},
{
"id": "Extension.extension",
"path": "Extension.extension",
"slicing": {
"discriminator": [
{
"type": "value",
"path": "url"
}
],
"ordered": false,
"rules": "open"
},
"min": 1,
"max": "*",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:type",
"path": "Extension.extension",
"sliceName": "type",
"short": "STU3: indel | snp | unknown (new)",
"definition": "STU3: `Sequence.quality.type` (new:code)",
"comment": "Element `Sequence.quality.type` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.type` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.type` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.type` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.type` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.type` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 1,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:type.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "type"
},
{
"id": "Extension.extension:type.value[x]",
"path": "Extension.extension.value[x]",
"short": "indel | snp | unknown",
"definition": "INDEL / SNP / Undefined variant.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "code"
}
],
"binding": {
"strength": "required",
"description": "Type for quality report",
"valueSet": "http://hl7.org/fhir/uv/xver/ValueSet/R3-quality-type-for-R5|0.1.0"
}
},
{
"id": "Extension.extension:standardSequence",
"path": "Extension.extension",
"sliceName": "standardSequence",
"short": "STU3: Standard sequence for comparison (new)",
"definition": "STU3: `Sequence.quality.standardSequence` (new:CodeableConcept)",
"comment": "Element `Sequence.quality.standardSequence` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.standardSequence` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.standardSequence` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.standardSequence` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.standardSequence` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.standardSequence` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:standardSequence.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "standardSequence"
},
{
"id": "Extension.extension:standardSequence.value[x]",
"path": "Extension.extension.value[x]",
"short": "Standard sequence for comparison",
"definition": "Gold standard sequence used for comparing against.",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Extension.extension:start",
"path": "Extension.extension",
"sliceName": "start",
"short": "STU3: Start position of the sequence (new)",
"definition": "STU3: `Sequence.quality.start` (new:integer)",
"comment": "Element `Sequence.quality.start` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.start` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.start` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.start` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.start` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.start` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:start.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "start"
},
{
"id": "Extension.extension:start.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
]
},
{
"id": "Extension.extension:end",
"path": "Extension.extension",
"sliceName": "end",
"short": "STU3: End position of the sequence (new)",
"definition": "STU3: `Sequence.quality.end` (new:integer)",
"comment": "Element `Sequence.quality.end` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.end` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.end` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.end` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.end` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.end` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:end.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "end"
},
{
"id": "Extension.extension:end.value[x]",
"path": "Extension.extension.value[x]",
"short": "End position of the sequence",
"definition": "End position of the sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "integer"
}
]
},
{
"id": "Extension.extension:score",
"path": "Extension.extension",
"sliceName": "score",
"short": "STU3: Quality score for the comparison (new)",
"definition": "STU3: `Sequence.quality.score` (new:Quantity)",
"comment": "Element `Sequence.quality.score` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.score` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.score` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.score` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.score` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.score` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:score.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "score"
},
{
"id": "Extension.extension:score.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "Quantity"
}
]
},
{
"id": "Extension.extension:method",
"path": "Extension.extension",
"sliceName": "method",
"short": "STU3: Method to get quality (new)",
"definition": "STU3: `Sequence.quality.method` (new:CodeableConcept)",
"comment": "Element `Sequence.quality.method` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.method` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.method` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.method` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.method` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.method` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:method.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "method"
},
{
"id": "Extension.extension:method.value[x]",
"path": "Extension.extension.value[x]",
"short": "Method to get quality",
"definition": "Which method is used to get sequence quality.",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Extension.extension:truthTP",
"path": "Extension.extension",
"sliceName": "truthTP",
"short": "STU3: True positives from the perspective of the truth data (new)",
"definition": "STU3: `Sequence.quality.truthTP` (new:decimal)",
"comment": "Element `Sequence.quality.truthTP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.truthTP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.truthTP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.truthTP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.truthTP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.truthTP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:truthTP.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "truthTP"
},
{
"id": "Extension.extension:truthTP.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
]
},
{
"id": "Extension.extension:queryTP",
"path": "Extension.extension",
"sliceName": "queryTP",
"short": "STU3: True positives from the perspective of the query data (new)",
"definition": "STU3: `Sequence.quality.queryTP` (new:decimal)",
"comment": "Element `Sequence.quality.queryTP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.queryTP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.queryTP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.queryTP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.queryTP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.queryTP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:queryTP.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "queryTP"
},
{
"id": "Extension.extension:queryTP.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
]
},
{
"id": "Extension.extension:truthFN",
"path": "Extension.extension",
"sliceName": "truthFN",
"short": "STU3: False negatives (new)",
"definition": "STU3: `Sequence.quality.truthFN` (new:decimal)",
"comment": "Element `Sequence.quality.truthFN` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.truthFN` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.truthFN` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.truthFN` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.truthFN` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.truthFN` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:truthFN.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "truthFN"
},
{
"id": "Extension.extension:truthFN.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
]
},
{
"id": "Extension.extension:queryFP",
"path": "Extension.extension",
"sliceName": "queryFP",
"short": "STU3: False positives (new)",
"definition": "STU3: `Sequence.quality.queryFP` (new:decimal)",
"comment": "Element `Sequence.quality.queryFP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.queryFP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.queryFP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.queryFP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.queryFP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.queryFP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:queryFP.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "queryFP"
},
{
"id": "Extension.extension:queryFP.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
]
},
{
"id": "Extension.extension:gtFP",
"path": "Extension.extension",
"sliceName": "gtFP",
"short": "STU3: False positives where the non-REF alleles in the Truth and Query Call Sets match (new)",
"definition": "STU3: `Sequence.quality.gtFP` (new:decimal)",
"comment": "Element `Sequence.quality.gtFP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.gtFP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.gtFP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.gtFP` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.gtFP` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.gtFP` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:gtFP.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "gtFP"
},
{
"id": "Extension.extension:gtFP.value[x]",
"path": "Extension.extension.value[x]",
"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": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
]
},
{
"id": "Extension.extension:precision",
"path": "Extension.extension",
"sliceName": "precision",
"short": "STU3: Precision of comparison (new)",
"definition": "STU3: `Sequence.quality.precision` (new:decimal)",
"comment": "Element `Sequence.quality.precision` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.precision` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.precision` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.precision` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.precision` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.precision` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:precision.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "precision"
},
{
"id": "Extension.extension:precision.value[x]",
"path": "Extension.extension.value[x]",
"short": "Precision of comparison",
"definition": "QUERY.TP / (QUERY.TP + QUERY.FP).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
]
},
{
"id": "Extension.extension:recall",
"path": "Extension.extension",
"sliceName": "recall",
"short": "STU3: Recall of comparison (new)",
"definition": "STU3: `Sequence.quality.recall` (new:decimal)",
"comment": "Element `Sequence.quality.recall` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.recall` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.recall` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.recall` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.recall` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.recall` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:recall.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "recall"
},
{
"id": "Extension.extension:recall.value[x]",
"path": "Extension.extension.value[x]",
"short": "Recall of comparison",
"definition": "TRUTH.TP / (TRUTH.TP + TRUTH.FN).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
]
},
{
"id": "Extension.extension:fScore",
"path": "Extension.extension",
"sliceName": "fScore",
"short": "STU3: F-score (new)",
"definition": "STU3: `Sequence.quality.fScore` (new:decimal)",
"comment": "Element `Sequence.quality.fScore` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.fScore` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.fScore` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"requirements": "Element `Sequence.quality.fScore` is part of an existing definition because parent element `Sequence.quality` requires a cross-version extension.\nElement `Sequence.quality.fScore` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.\nElement `Sequence.quality.fScore` has no mapping targets in FHIR R5. Typically, this is because the element has been added (is a new element).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.extension",
"min": 0,
"max": "*"
}
},
{
"id": "Extension.extension:fScore.url",
"path": "Extension.extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "fScore"
},
{
"id": "Extension.extension:fScore.value[x]",
"path": "Extension.extension.value[x]",
"short": "F-score",
"definition": "Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).",
"min": 0,
"max": "1",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
},
"type": [
{
"code": "decimal"
}
]
},
{
"id": "Extension.url",
"path": "Extension.url",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"fixedUri": "http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.quality"
},
{
"id": "Extension.value[x]",
"path": "Extension.value[x]",
"min": 0,
"max": "0",
"base": {
"path": "Extension.value[x]",
"min": 0,
"max": "1"
}
}
]
}
}