| Package | hl7.fhir.uv.xver-r4.r5 |
| Type | StructureDefinition |
| Id | Id |
| FHIR Version | R5 |
| Source | http://hl7.org/fhir/uv/xver/https://simplifier.net/resolve?scope=hl7.fhir.uv.xver-r4.r5@0.0.1-snapshot-1&canonical=http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.quality |
| Url | http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.quality |
| Version | 0.0.1-snapshot-1 |
| Status | draft |
| Date | 2025-06-03T03:13:07.4212066+02:00 |
| Name | ext_R4_MolecularSequence_quality |
| Title | Cross-version Extension for R4.MolecularSequence.quality for use in FHIR R5 |
| Experimental | False |
| Realm | uv |
| Authority | hl7 |
| Description | This cross-version extension represents MolecularSequence.quality from http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.0.1 for use in FHIR R5. |
| Type | Extension |
| Kind | complex-type |
No resources found
| ValueSet | |
http://hl7.org/fhir/uv/xver/4.0/ValueSet/R4-quality-type-for-R5  | Cross-version VS for R4.qualityType for use in FHIR R5 |
FHIR{
"resourceType" : "StructureDefinition",
"id" : "ext-R4-MolecularSequence.quality",
"url" : "http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.quality",
"version" : "0.0.1-snapshot-1",
"name" : "ext_R4_MolecularSequence_quality",
"title" : "Cross-version Extension for R4.MolecularSequence.quality for use in FHIR R5",
"status" : "draft",
"experimental" : false,
"date" : "2025-06-03T03:13:07.4212066+02:00",
"description" : "This cross-version extension represents MolecularSequence.quality from http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.0.1 for use in FHIR R5.",
"fhirVersion" : "5.0.0",
"kind" : "complex-type",
"abstract" : false,
"context" : [
{
"type" : "element",
"expression" : "MolecularSequence"
}
],
"type" : "Extension",
"baseDefinition" : "http://hl7.org/fhir/StructureDefinition/Extension",
"derivation" : "constraint",
"snapshot" : {
"element" : [
{
"id" : "Extension",
"path" : "Extension",
"short" : "An set of value as quality of sequence",
"definition" : "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "*",
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{
"key" : "ext-1",
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"min" : 0,
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{
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"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
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"code" : "http://hl7.org/fhirpath/System.String"
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"isModifier" : false,
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"ordered" : false,
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"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",
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"min" : 1,
"max" : "*",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
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"type" : [
{
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],
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{
"key" : "ele-1",
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"expression" : "hasValue() or (children().count() > id.count())",
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{
"key" : "ext-1",
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],
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},
{
"id" : "Extension.extension:type",
"path" : "Extension.extension",
"sliceName" : "type",
"short" : "indel | snp | unknown",
"definition" : "INDEL / SNP / Undefined variant.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
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"extensions",
"user content"
],
"min" : 1,
"max" : "1",
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{
"key" : "ele-1",
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"expression" : "hasValue() or (children().count() > id.count())",
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{
"key" : "ext-1",
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"expression" : "extension.exists() != value.exists()",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
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{
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]
},
{
"id" : "Extension.extension:type.id",
"path" : "Extension.extension.id",
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"xmlAttr"
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"short" : "Unique id for inter-element referencing",
"definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.id",
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"max" : "1"
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"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "id"
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],
"code" : "http://hl7.org/fhirpath/System.String"
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"mapping" : [
{
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{
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"path" : "Extension.extension.extension",
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{
"type" : "value",
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"rules" : "open"
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"short" : "Additional content defined by implementations",
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"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",
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"expression" : "hasValue() or (children().count() > id.count())",
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},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
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}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
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}
]
},
{
"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.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "code"
}
],
"condition" : [
"ext-1"
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"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
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"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"binding" : {
"strength" : "required",
"description" : "Type for quality report.",
"valueSet" : "http://hl7.org/fhir/uv/xver/4.0/ValueSet/R4-quality-type-for-R5"
},
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:standardSequence",
"path" : "Extension.extension",
"sliceName" : "standardSequence",
"short" : "Standard sequence for comparison",
"definition" : "Gold standard sequence used for comparing against.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"alias" : [
"extensions",
"user content"
],
"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"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
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}
],
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"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"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"
},
{
"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"
}
],
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"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.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "CodeableConcept"
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],
"condition" : [
"ext-1"
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"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"binding" : {
"strength" : "example",
"description" : "Reference identifier of the sequence that used to mark the quality of tested samples.",
"valueSet" : "http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence"
},
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:start",
"path" : "Extension.extension",
"sliceName" : "start",
"short" : "Start position of the sequence",
"definition" : "Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"alias" : [
"extensions",
"user content"
],
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
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],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
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}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"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"
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"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "id"
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],
"code" : "http://hl7.org/fhirpath/System.String"
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],
"condition" : [
"ele-1"
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"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
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]
},
{
"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"
},
{
"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"
}
],
"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.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "integer"
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:end",
"path" : "Extension.extension",
"sliceName" : "end",
"short" : "End position of the sequence",
"definition" : "End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"alias" : [
"extensions",
"user content"
],
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"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"
},
{
"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"
}
],
"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 exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "integer"
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:score",
"path" : "Extension.extension",
"sliceName" : "score",
"short" : "Quality score for the comparison",
"definition" : "The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"alias" : [
"extensions",
"user content"
],
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"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"
},
{
"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"
}
],
"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)).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:method",
"path" : "Extension.extension",
"sliceName" : "method",
"short" : "Method to get quality",
"definition" : "Which method is used to get sequence quality.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"alias" : [
"extensions",
"user content"
],
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"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"
},
{
"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"
}
],
"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.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "CodeableConcept"
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"binding" : {
"strength" : "example",
"description" : "The method used to evaluate the numerical quality of the observed sequence.",
"valueSet" : "http://hl7.org/fhir/ValueSet/sequence-quality-method"
},
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:truthTP",
"path" : "Extension.extension",
"sliceName" : "truthTP",
"short" : "True positives from the perspective of the truth data",
"definition" : "True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"alias" : [
"extensions",
"user content"
],
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"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"
},
{
"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"
}
],
"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.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:queryTP",
"path" : "Extension.extension",
"sliceName" : "queryTP",
"short" : "True positives from the perspective of the query data",
"definition" : "True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"alias" : [
"extensions",
"user content"
],
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"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"
},
{
"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"
}
],
"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.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:truthFN",
"path" : "Extension.extension",
"sliceName" : "truthFN",
"short" : "False negatives",
"definition" : "False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"alias" : [
"extensions",
"user content"
],
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"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"
},
{
"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"
}
],
"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.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:queryFP",
"path" : "Extension.extension",
"sliceName" : "queryFP",
"short" : "False positives",
"definition" : "False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"alias" : [
"extensions",
"user content"
],
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"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,
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:score",
"path" : "Extension.extension.extension",
"sliceName" : "score",
"short" : "Genotype quality score",
"definition" : "Invidual data point representing the GQ (genotype quality) score threshold.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:score.id",
"path" : "Extension.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:roc.extension:score.extension",
"path" : "Extension.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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:score.url",
"path" : "Extension.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:roc.extension:score.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "Genotype quality score",
"definition" : "Invidual data point representing the GQ (genotype quality) score threshold.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "integer"
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:roc.extension:numTP",
"path" : "Extension.extension.extension",
"sliceName" : "numTP",
"short" : "Roc score true positive numbers",
"definition" : "The number of true positives if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:numTP.id",
"path" : "Extension.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:roc.extension:numTP.extension",
"path" : "Extension.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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:numTP.url",
"path" : "Extension.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" : "numTP",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:roc.extension:numTP.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "Roc score true positive numbers",
"definition" : "The number of true positives if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "integer"
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:roc.extension:numFP",
"path" : "Extension.extension.extension",
"sliceName" : "numFP",
"short" : "Roc score false positive numbers",
"definition" : "The number of false positives if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:numFP.id",
"path" : "Extension.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:roc.extension:numFP.extension",
"path" : "Extension.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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:numFP.url",
"path" : "Extension.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" : "numFP",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:roc.extension:numFP.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "Roc score false positive numbers",
"definition" : "The number of false positives if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "integer"
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:roc.extension:numFN",
"path" : "Extension.extension.extension",
"sliceName" : "numFN",
"short" : "Roc score false negative numbers",
"definition" : "The number of false negatives if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:numFN.id",
"path" : "Extension.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:roc.extension:numFN.extension",
"path" : "Extension.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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:numFN.url",
"path" : "Extension.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" : "numFN",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:roc.extension:numFN.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "Roc score false negative numbers",
"definition" : "The number of false negatives if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "integer"
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:roc.extension:precision",
"path" : "Extension.extension.extension",
"sliceName" : "precision",
"short" : "Precision of the GQ score",
"definition" : "Calculated precision if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:precision.id",
"path" : "Extension.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:roc.extension:precision.extension",
"path" : "Extension.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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:precision.url",
"path" : "Extension.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:roc.extension:precision.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "Precision of the GQ score",
"definition" : "Calculated precision if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:roc.extension:sensitivity",
"path" : "Extension.extension.extension",
"sliceName" : "sensitivity",
"short" : "Sensitivity of the GQ score",
"definition" : "Calculated sensitivity if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:sensitivity.id",
"path" : "Extension.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:roc.extension:sensitivity.extension",
"path" : "Extension.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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:sensitivity.url",
"path" : "Extension.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" : "sensitivity",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:roc.extension:sensitivity.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "Sensitivity of the GQ score",
"definition" : "Calculated sensitivity if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:roc.extension:fMeasure",
"path" : "Extension.extension.extension",
"sliceName" : "fMeasure",
"short" : "FScore of the GQ score",
"definition" : "Calculated fScore if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:fMeasure.id",
"path" : "Extension.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:roc.extension:fMeasure.extension",
"path" : "Extension.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"
},
{
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:roc.extension:fMeasure.url",
"path" : "Extension.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" : "fMeasure",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:roc.extension:fMeasure.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "FScore of the GQ score",
"definition" : "Calculated fScore if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:roc.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" : "roc",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:roc.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Value of extension",
"definition" : "Value of extension - must be one of a constrained set of the data types (see [Extensibility](extensibility.html) for a list).",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "base64Binary"
},
{
"code" : "boolean"
},
{
"code" : "canonical"
},
{
"code" : "code"
},
{
"code" : "date"
},
{
"code" : "dateTime"
},
{
"code" : "decimal"
},
{
"code" : "id"
},
{
"code" : "instant"
},
{
"code" : "integer"
},
{
"code" : "integer64"
},
{
"code" : "markdown"
},
{
"code" : "oid"
},
{
"code" : "positiveInt"
},
{
"code" : "string"
},
{
"code" : "time"
},
{
"code" : "unsignedInt"
},
{
"code" : "uri"
},
{
"code" : "url"
},
{
"code" : "uuid"
},
{
"code" : "Address"
},
{
"code" : "Age"
},
{
"code" : "Annotation"
},
{
"code" : "Attachment"
},
{
"code" : "CodeableConcept"
},
{
"code" : "CodeableReference"
},
{
"code" : "Coding"
},
{
"code" : "ContactPoint"
},
{
"code" : "Count"
},
{
"code" : "Distance"
},
{
"code" : "Duration"
},
{
"code" : "HumanName"
},
{
"code" : "Identifier"
},
{
"code" : "Money"
},
{
"code" : "Period"
},
{
"code" : "Quantity"
},
{
"code" : "Range"
},
{
"code" : "Ratio"
},
{
"code" : "RatioRange"
},
{
"code" : "Reference"
},
{
"code" : "SampledData"
},
{
"code" : "Signature"
},
{
"code" : "Timing"
},
{
"code" : "ContactDetail"
},
{
"code" : "DataRequirement"
},
{
"code" : "Expression"
},
{
"code" : "ParameterDefinition"
},
{
"code" : "RelatedArtifact"
},
{
"code" : "TriggerDefinition"
},
{
"code" : "UsageContext"
},
{
"code" : "Availability"
},
{
"code" : "ExtendedContactDetail"
},
{
"code" : "Dosage"
},
{
"code" : "Meta"
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.url",
"path" : "Extension.url",
"representation" : [
"xmlAttr"
],
"short" : "identifies the meaning of the extension",
"definition" : "Source of the definition for the extension code - a logical name or a URL.",
"comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min" : 1,
"max" : "1",
"base" : {
"path" : "Extension.url",
"min" : 1,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "uri"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri" : "http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.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](extensibility.html) for a list).",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "base64Binary"
},
{
"code" : "boolean"
},
{
"code" : "canonical"
},
{
"code" : "code"
},
{
"code" : "date"
},
{
"code" : "dateTime"
},
{
"code" : "decimal"
},
{
"code" : "id"
},
{
"code" : "instant"
},
{
"code" : "integer"
},
{
"code" : "integer64"
},
{
"code" : "markdown"
},
{
"code" : "oid"
},
{
"code" : "positiveInt"
},
{
"code" : "string"
},
{
"code" : "time"
},
{
"code" : "unsignedInt"
},
{
"code" : "uri"
},
{
"code" : "url"
},
{
"code" : "uuid"
},
{
"code" : "Address"
},
{
"code" : "Age"
},
{
"code" : "Annotation"
},
{
"code" : "Attachment"
},
{
"code" : "CodeableConcept"
},
{
"code" : "CodeableReference"
},
{
"code" : "Coding"
},
{
"code" : "ContactPoint"
},
{
"code" : "Count"
},
{
"code" : "Distance"
},
{
"code" : "Duration"
},
{
"code" : "HumanName"
},
{
"code" : "Identifier"
},
{
"code" : "Money"
},
{
"code" : "Period"
},
{
"code" : "Quantity"
},
{
"code" : "Range"
},
{
"code" : "Ratio"
},
{
"code" : "RatioRange"
},
{
"code" : "Reference"
},
{
"code" : "SampledData"
},
{
"code" : "Signature"
},
{
"code" : "Timing"
},
{
"code" : "ContactDetail"
},
{
"code" : "DataRequirement"
},
{
"code" : "Expression"
},
{
"code" : "ParameterDefinition"
},
{
"code" : "RelatedArtifact"
},
{
"code" : "TriggerDefinition"
},
{
"code" : "UsageContext"
},
{
"code" : "Availability"
},
{
"code" : "ExtendedContactDetail"
},
{
"code" : "Dosage"
},
{
"code" : "Meta"
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
}
]
},
"differential" : {
"element" : [
{
"id" : "Extension",
"path" : "Extension",
"short" : "An set of value as quality of sequence",
"definition" : "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "*",
"isModifier" : false
},
{
"id" : "Extension.extension",
"path" : "Extension.extension",
"slicing" : {
"discriminator" : [
{
"type" : "value",
"path" : "url"
}
],
"ordered" : false,
"rules" : "closed"
},
"min" : 1,
"max" : "*"
},
{
"id" : "Extension.extension:type",
"path" : "Extension.extension",
"sliceName" : "type",
"short" : "indel | snp | unknown",
"definition" : "INDEL / SNP / Undefined variant.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 1,
"max" : "1",
"isModifier" : false
},
{
"id" : "Extension.extension:type.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "indel | snp | unknown",
"definition" : "INDEL / SNP / Undefined variant.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "code"
}
],
"binding" : {
"strength" : "required",
"description" : "Type for quality report.",
"valueSet" : "http://hl7.org/fhir/uv/xver/4.0/ValueSet/R4-quality-type-for-R5"
}
},
{
"id" : "Extension.extension:standardSequence",
"path" : "Extension.extension",
"sliceName" : "standardSequence",
"short" : "Standard sequence for comparison",
"definition" : "Gold standard sequence used for comparing against.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"id" : "Extension.extension:standardSequence.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Standard sequence for comparison",
"definition" : "Gold standard sequence used for comparing against.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "CodeableConcept"
}
],
"binding" : {
"strength" : "example",
"description" : "Reference identifier of the sequence that used to mark the quality of tested samples.",
"valueSet" : "http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence"
}
},
{
"id" : "Extension.extension:start",
"path" : "Extension.extension",
"sliceName" : "start",
"short" : "Start position of the sequence",
"definition" : "Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"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.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "integer"
}
]
},
{
"id" : "Extension.extension:end",
"path" : "Extension.extension",
"sliceName" : "end",
"short" : "End position of the sequence",
"definition" : "End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"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 exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "integer"
}
]
},
{
"id" : "Extension.extension:score",
"path" : "Extension.extension",
"sliceName" : "score",
"short" : "Quality score for the comparison",
"definition" : "The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"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)).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "Quantity"
}
]
},
{
"id" : "Extension.extension:method",
"path" : "Extension.extension",
"sliceName" : "method",
"short" : "Method to get quality",
"definition" : "Which method is used to get sequence quality.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"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.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "CodeableConcept"
}
],
"binding" : {
"strength" : "example",
"description" : "The method used to evaluate the numerical quality of the observed sequence.",
"valueSet" : "http://hl7.org/fhir/ValueSet/sequence-quality-method"
}
},
{
"id" : "Extension.extension:truthTP",
"path" : "Extension.extension",
"sliceName" : "truthTP",
"short" : "True positives from the perspective of the truth data",
"definition" : "True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"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.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "decimal"
}
]
},
{
"id" : "Extension.extension:queryTP",
"path" : "Extension.extension",
"sliceName" : "queryTP",
"short" : "True positives from the perspective of the query data",
"definition" : "True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"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.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "decimal"
}
]
},
{
"id" : "Extension.extension:truthFN",
"path" : "Extension.extension",
"sliceName" : "truthFN",
"short" : "False negatives",
"definition" : "False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"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.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "decimal"
}
]
},
{
"id" : "Extension.extension:queryFP",
"path" : "Extension.extension",
"sliceName" : "queryFP",
"short" : "False positives",
"definition" : "False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"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.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "decimal"
}
]
},
{
"id" : "Extension.extension:gtFP",
"path" : "Extension.extension",
"sliceName" : "gtFP",
"short" : "False positives where the non-REF alleles in the Truth and Query Call Sets match",
"definition" : "The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"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).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "decimal"
}
]
},
{
"id" : "Extension.extension:precision",
"path" : "Extension.extension",
"sliceName" : "precision",
"short" : "Precision of comparison",
"definition" : "QUERY.TP / (QUERY.TP + QUERY.FP).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"id" : "Extension.extension:precision.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Precision of comparison",
"definition" : "QUERY.TP / (QUERY.TP + QUERY.FP).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "decimal"
}
]
},
{
"id" : "Extension.extension:recall",
"path" : "Extension.extension",
"sliceName" : "recall",
"short" : "Recall of comparison",
"definition" : "TRUTH.TP / (TRUTH.TP + TRUTH.FN).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"id" : "Extension.extension:recall.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Recall of comparison",
"definition" : "TRUTH.TP / (TRUTH.TP + TRUTH.FN).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "decimal"
}
]
},
{
"id" : "Extension.extension:fScore",
"path" : "Extension.extension",
"sliceName" : "fScore",
"short" : "F-score",
"definition" : "Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"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).",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "decimal"
}
]
},
{
"id" : "Extension.extension:roc",
"path" : "Extension.extension",
"sliceName" : "roc",
"short" : "Receiver Operator Characteristic (ROC) Curve",
"definition" : "Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"id" : "Extension.extension:roc.extension",
"path" : "Extension.extension.extension",
"slicing" : {
"discriminator" : [
{
"type" : "value",
"path" : "url"
}
],
"ordered" : false,
"rules" : "closed"
},
"min" : 0,
"max" : "*"
},
{
"id" : "Extension.extension:roc.extension:score",
"path" : "Extension.extension.extension",
"sliceName" : "score",
"short" : "Genotype quality score",
"definition" : "Invidual data point representing the GQ (genotype quality) score threshold.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "*",
"isModifier" : false
},
{
"id" : "Extension.extension:roc.extension:score.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "Genotype quality score",
"definition" : "Invidual data point representing the GQ (genotype quality) score threshold.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "integer"
}
]
},
{
"id" : "Extension.extension:roc.extension:numTP",
"path" : "Extension.extension.extension",
"sliceName" : "numTP",
"short" : "Roc score true positive numbers",
"definition" : "The number of true positives if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "*",
"isModifier" : false
},
{
"id" : "Extension.extension:roc.extension:numTP.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "Roc score true positive numbers",
"definition" : "The number of true positives if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "integer"
}
]
},
{
"id" : "Extension.extension:roc.extension:numFP",
"path" : "Extension.extension.extension",
"sliceName" : "numFP",
"short" : "Roc score false positive numbers",
"definition" : "The number of false positives if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "*",
"isModifier" : false
},
{
"id" : "Extension.extension:roc.extension:numFP.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "Roc score false positive numbers",
"definition" : "The number of false positives if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "integer"
}
]
},
{
"id" : "Extension.extension:roc.extension:numFN",
"path" : "Extension.extension.extension",
"sliceName" : "numFN",
"short" : "Roc score false negative numbers",
"definition" : "The number of false negatives if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "*",
"isModifier" : false
},
{
"id" : "Extension.extension:roc.extension:numFN.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "Roc score false negative numbers",
"definition" : "The number of false negatives if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "integer"
}
]
},
{
"id" : "Extension.extension:roc.extension:precision",
"path" : "Extension.extension.extension",
"sliceName" : "precision",
"short" : "Precision of the GQ score",
"definition" : "Calculated precision if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "*",
"isModifier" : false
},
{
"id" : "Extension.extension:roc.extension:precision.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "Precision of the GQ score",
"definition" : "Calculated precision if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "decimal"
}
]
},
{
"id" : "Extension.extension:roc.extension:sensitivity",
"path" : "Extension.extension.extension",
"sliceName" : "sensitivity",
"short" : "Sensitivity of the GQ score",
"definition" : "Calculated sensitivity if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "*",
"isModifier" : false
},
{
"id" : "Extension.extension:roc.extension:sensitivity.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "Sensitivity of the GQ score",
"definition" : "Calculated sensitivity if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "decimal"
}
]
},
{
"id" : "Extension.extension:roc.extension:fMeasure",
"path" : "Extension.extension.extension",
"sliceName" : "fMeasure",
"short" : "FScore of the GQ score",
"definition" : "Calculated fScore if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "*",
"isModifier" : false
},
{
"id" : "Extension.extension:roc.extension:fMeasure.value[x]",
"path" : "Extension.extension.extension.value[x]",
"short" : "FScore of the GQ score",
"definition" : "Calculated fScore if the GQ score threshold was set to \"score\" field value.",
"comment" : "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "decimal"
}
]
},
{
"id" : "Extension.url",
"path" : "Extension.url",
"min" : 1,
"max" : "1",
"fixedUri" : "http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.quality"
}
]
},
"text" : {
}
}
XIG built as of ??metadata-date??. Found ??metadata-resources?? resources in ??metadata-packages?? packages.