{
"description": "This cross-version extension represents MolecularSequence.quality from http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.0.1 for use in FHIR R5.",
"_filename": "StructureDefinition-ext-R4-MolecularSequence.quality.json",
"package_name": "hl7.fhir.uv.xver",
"date": "2025-09-01T22:36:30.980483+10:00",
"derivation": "constraint",
"publisher": "FHIR Infrastructure",
"fhirVersion": "5.0.0",
"jurisdiction": [ {
"coding": [ {
"code": "001",
"system": "http://unstats.un.org/unsd/methods/m49/m49.htm",
"display": "World"
} ]
} ],
"name": "Ext_R4_MolecularSequence_quality",
"mapping": [ {
"uri": "http://hl7.org/v3",
"name": "RIM Mapping",
"identity": "rim"
} ],
"abstract": false,
"type": "Extension",
"experimental": "false",
"resourceType": "StructureDefinition",
"title": "Cross-version Extension for R4.MolecularSequence.quality for use in FHIR R5",
"package_version": "r4.r5-0.0.1-snapshot-2",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode": "fhir"
}, {
"url": "http://hl7.org/fhir/StructureDefinition/package-source",
"extension": [ {
"url": "packageId",
"valueId": "hl7.fhir.uv.xver-r4.r5"
}, {
"url": "version",
"valueString": "0.0.1-snapshot-2"
} ]
}, {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-type-characteristics",
"valueCode": "can-bind"
}, {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
"valueInteger": 0,
"_valueInteger": {
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
"valueCanonical": "http://hl7.org/fhir/4.0/ImplementationGuide/hl7.fhir.uv.xver-r4.r5"
} ]
}
}, {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
"valueCode": "trial-use",
"_valueCode": {
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
"valueCanonical": "http://hl7.org/fhir/4.0/ImplementationGuide/hl7.fhir.uv.xver-r4.r5"
} ]
}
} ],
"snapshot": {
"element": [ {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension",
"min": 0,
"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)).",
"isModifier": false,
"short": "An set of value as quality of sequence",
"max": "*",
"id": "Extension",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension"
}
}, {
"path": "Extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 1,
"definition": "An Extension",
"isModifier": false,
"short": "Extension",
"slicing": {
"rules": "closed",
"ordered": false,
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"max": "*",
"id": "Extension.extension",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 1,
"definition": "INDEL / SNP / Undefined variant.",
"isModifier": false,
"short": "indel | snp | unknown",
"type": [ {
"code": "Extension"
} ],
"sliceName": "type",
"max": "1",
"id": "Extension.extension:type",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:type.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:type.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "type",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:type.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"definition": "INDEL / SNP / Undefined variant.",
"isModifier": false,
"short": "indel | snp | unknown",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "code"
} ],
"binding": {
"strength": "required",
"valueSet": "http://hl7.org/fhir/4.0/ValueSet/R4-quality-type-for-R5|0.0.1-snapshot-2",
"description": "Type for quality report."
},
"max": "1",
"id": "Extension.extension:type.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"definition": "Gold standard sequence used for comparing against.",
"isModifier": false,
"short": "Standard sequence for comparison",
"type": [ {
"code": "Extension"
} ],
"sliceName": "standardSequence",
"max": "1",
"id": "Extension.extension:standardSequence",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:standardSequence.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:standardSequence.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "standardSequence",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:standardSequence.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"definition": "Gold standard sequence used for comparing against.",
"isModifier": false,
"short": "Standard sequence for comparison",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "CodeableConcept"
} ],
"binding": {
"strength": "example",
"valueSet": "http://hl7.org/fhir/4.0/ValueSet/R4-sequence-quality-standardSequence-for-R5|0.0.1-snapshot-2",
"description": "Reference identifier of the sequence that used to mark the quality of tested samples."
},
"max": "1",
"id": "Extension.extension:standardSequence.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"definition": "Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"isModifier": false,
"short": "Start position of the sequence",
"type": [ {
"code": "Extension"
} ],
"sliceName": "start",
"max": "1",
"id": "Extension.extension:start",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:start.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:start.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "start",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:start.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"definition": "Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"isModifier": false,
"short": "Start position of the sequence",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "integer"
} ],
"max": "1",
"id": "Extension.extension:start.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "End position of the sequence",
"type": [ {
"code": "Extension"
} ],
"sliceName": "end",
"max": "1",
"id": "Extension.extension:end",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:end.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:end.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "end",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:end.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"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.",
"isModifier": false,
"short": "End position of the sequence",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "integer"
} ],
"max": "1",
"id": "Extension.extension:end.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"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)).",
"isModifier": false,
"short": "Quality score for the comparison",
"type": [ {
"code": "Extension"
} ],
"sliceName": "score",
"max": "1",
"id": "Extension.extension:score",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:score.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:score.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "score",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:score.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"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)).",
"isModifier": false,
"short": "Quality score for the comparison",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Quantity"
} ],
"max": "1",
"id": "Extension.extension:score.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"definition": "Which method is used to get sequence quality.",
"isModifier": false,
"short": "Method to get quality",
"type": [ {
"code": "Extension"
} ],
"sliceName": "method",
"max": "1",
"id": "Extension.extension:method",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:method.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:method.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "method",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:method.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"definition": "Which method is used to get sequence quality.",
"isModifier": false,
"short": "Method to get quality",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "CodeableConcept"
} ],
"binding": {
"strength": "example",
"valueSet": "http://hl7.org/fhir/4.0/ValueSet/R4-sequence-quality-method-for-R5|0.0.1-snapshot-2",
"description": "The method used to evaluate the numerical quality of the observed sequence."
},
"max": "1",
"id": "Extension.extension:method.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "True positives from the perspective of the truth data",
"type": [ {
"code": "Extension"
} ],
"sliceName": "truthTP",
"max": "1",
"id": "Extension.extension:truthTP",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:truthTP.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:truthTP.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "truthTP",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:truthTP.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"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.",
"isModifier": false,
"short": "True positives from the perspective of the truth data",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "decimal"
} ],
"max": "1",
"id": "Extension.extension:truthTP.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "True positives from the perspective of the query data",
"type": [ {
"code": "Extension"
} ],
"sliceName": "queryTP",
"max": "1",
"id": "Extension.extension:queryTP",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:queryTP.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:queryTP.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "queryTP",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:queryTP.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"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.",
"isModifier": false,
"short": "True positives from the perspective of the query data",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "decimal"
} ],
"max": "1",
"id": "Extension.extension:queryTP.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "False negatives",
"type": [ {
"code": "Extension"
} ],
"sliceName": "truthFN",
"max": "1",
"id": "Extension.extension:truthFN",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:truthFN.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:truthFN.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "truthFN",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:truthFN.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"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.",
"isModifier": false,
"short": "False negatives",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "decimal"
} ],
"max": "1",
"id": "Extension.extension:truthFN.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "False positives",
"type": [ {
"code": "Extension"
} ],
"sliceName": "queryFP",
"max": "1",
"id": "Extension.extension:queryFP",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:queryFP.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:queryFP.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "queryFP",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:queryFP.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"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.",
"isModifier": false,
"short": "False positives",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "decimal"
} ],
"max": "1",
"id": "Extension.extension:queryFP.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"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).",
"isModifier": false,
"short": "False positives where the non-REF alleles in the Truth and Query Call Sets match",
"type": [ {
"code": "Extension"
} ],
"sliceName": "gtFP",
"max": "1",
"id": "Extension.extension:gtFP",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:gtFP.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:gtFP.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "gtFP",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:gtFP.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"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).",
"isModifier": false,
"short": "False positives where the non-REF alleles in the Truth and Query Call Sets match",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "decimal"
} ],
"max": "1",
"id": "Extension.extension:gtFP.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"definition": "QUERY.TP / (QUERY.TP + QUERY.FP).",
"isModifier": false,
"short": "Precision of comparison",
"type": [ {
"code": "Extension"
} ],
"sliceName": "precision",
"max": "1",
"id": "Extension.extension:precision",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:precision.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:precision.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "precision",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:precision.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"definition": "QUERY.TP / (QUERY.TP + QUERY.FP).",
"isModifier": false,
"short": "Precision of comparison",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "decimal"
} ],
"max": "1",
"id": "Extension.extension:precision.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"definition": "TRUTH.TP / (TRUTH.TP + TRUTH.FN).",
"isModifier": false,
"short": "Recall of comparison",
"type": [ {
"code": "Extension"
} ],
"sliceName": "recall",
"max": "1",
"id": "Extension.extension:recall",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:recall.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:recall.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "recall",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:recall.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"definition": "TRUTH.TP / (TRUTH.TP + TRUTH.FN).",
"isModifier": false,
"short": "Recall of comparison",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "decimal"
} ],
"max": "1",
"id": "Extension.extension:recall.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"definition": "Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).",
"isModifier": false,
"short": "F-score",
"type": [ {
"code": "Extension"
} ],
"sliceName": "fScore",
"max": "1",
"id": "Extension.extension:fScore",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:fScore.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:fScore.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "fScore",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:fScore.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"definition": "Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).",
"isModifier": false,
"short": "F-score",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "decimal"
} ],
"max": "1",
"id": "Extension.extension:fScore.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension",
"min": 0,
"definition": "Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.",
"isModifier": false,
"short": "Receiver Operator Characteristic (ROC) Curve",
"type": [ {
"code": "Extension"
} ],
"sliceName": "roc",
"max": "1",
"id": "Extension.extension:roc",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"definition": "An Extension",
"isModifier": false,
"short": "Extension",
"slicing": {
"rules": "closed",
"ordered": false,
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"max": "*",
"id": "Extension.extension:roc.extension",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"definition": "Invidual data point representing the GQ (genotype quality) score threshold.",
"isModifier": false,
"short": "Genotype quality score",
"type": [ {
"code": "Extension"
} ],
"sliceName": "score",
"max": "*",
"id": "Extension.extension:roc.extension:score",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:score.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:roc.extension:score.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "score",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:score.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.extension.value[x]",
"min": 0,
"definition": "Invidual data point representing the GQ (genotype quality) score threshold.",
"isModifier": false,
"short": "Genotype quality score",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "integer"
} ],
"max": "1",
"id": "Extension.extension:roc.extension:score.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"definition": "The number of true positives if the GQ score threshold was set to \"score\" field value.",
"isModifier": false,
"short": "Roc score true positive numbers",
"type": [ {
"code": "Extension"
} ],
"sliceName": "numTP",
"max": "*",
"id": "Extension.extension:roc.extension:numTP",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:numTP.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:roc.extension:numTP.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "numTP",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:numTP.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.extension.value[x]",
"min": 0,
"definition": "The number of true positives if the GQ score threshold was set to \"score\" field value.",
"isModifier": false,
"short": "Roc score true positive numbers",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "integer"
} ],
"max": "1",
"id": "Extension.extension:roc.extension:numTP.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"definition": "The number of false positives if the GQ score threshold was set to \"score\" field value.",
"isModifier": false,
"short": "Roc score false positive numbers",
"type": [ {
"code": "Extension"
} ],
"sliceName": "numFP",
"max": "*",
"id": "Extension.extension:roc.extension:numFP",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:numFP.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:roc.extension:numFP.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "numFP",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:numFP.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.extension.value[x]",
"min": 0,
"definition": "The number of false positives if the GQ score threshold was set to \"score\" field value.",
"isModifier": false,
"short": "Roc score false positive numbers",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "integer"
} ],
"max": "1",
"id": "Extension.extension:roc.extension:numFP.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"definition": "The number of false negatives if the GQ score threshold was set to \"score\" field value.",
"isModifier": false,
"short": "Roc score false negative numbers",
"type": [ {
"code": "Extension"
} ],
"sliceName": "numFN",
"max": "*",
"id": "Extension.extension:roc.extension:numFN",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:numFN.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:roc.extension:numFN.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "numFN",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:numFN.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.extension.value[x]",
"min": 0,
"definition": "The number of false negatives if the GQ score threshold was set to \"score\" field value.",
"isModifier": false,
"short": "Roc score false negative numbers",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "integer"
} ],
"max": "1",
"id": "Extension.extension:roc.extension:numFN.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"definition": "Calculated precision if the GQ score threshold was set to \"score\" field value.",
"isModifier": false,
"short": "Precision of the GQ score",
"type": [ {
"code": "Extension"
} ],
"sliceName": "precision",
"max": "*",
"id": "Extension.extension:roc.extension:precision",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:precision.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:roc.extension:precision.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "precision",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:precision.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.extension.value[x]",
"min": 0,
"definition": "Calculated precision if the GQ score threshold was set to \"score\" field value.",
"isModifier": false,
"short": "Precision of the GQ score",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "decimal"
} ],
"max": "1",
"id": "Extension.extension:roc.extension:precision.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"definition": "Calculated sensitivity if the GQ score threshold was set to \"score\" field value.",
"isModifier": false,
"short": "Sensitivity of the GQ score",
"type": [ {
"code": "Extension"
} ],
"sliceName": "sensitivity",
"max": "*",
"id": "Extension.extension:roc.extension:sensitivity",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:sensitivity.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:roc.extension:sensitivity.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "sensitivity",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:sensitivity.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.extension.value[x]",
"min": 0,
"definition": "Calculated sensitivity if the GQ score threshold was set to \"score\" field value.",
"isModifier": false,
"short": "Sensitivity of the GQ score",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "decimal"
} ],
"max": "1",
"id": "Extension.extension:roc.extension:sensitivity.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension",
"min": 0,
"definition": "Calculated fScore if the GQ score threshold was set to \"score\" field value.",
"isModifier": false,
"short": "FScore of the GQ score",
"type": [ {
"code": "Extension"
} ],
"sliceName": "fMeasure",
"max": "*",
"id": "Extension.extension:roc.extension:fMeasure",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.id",
"min": 0,
"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"isModifier": false,
"short": "Unique id for inter-element referencing",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "id"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:fMeasure.id",
"condition": [ "ele-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"source": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension.extension.extension.extension",
"min": 0,
"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.",
"isModifier": false,
"short": "Additional content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"slicing": {
"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.extension:roc.extension:fMeasure.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
},
"isSummary": false
}, {
"path": "Extension.extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "fMeasure",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.extension:fMeasure.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.extension.value[x]",
"min": 0,
"definition": "Calculated fScore if the GQ score threshold was set to \"score\" field value.",
"isModifier": false,
"short": "FScore of the GQ score",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "decimal"
} ],
"max": "1",
"id": "Extension.extension:roc.extension:fMeasure.value[x]",
"condition": [ "ext-1" ],
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "roc",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:roc.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.extension.value[x]",
"min": 0,
"definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R5/extensibility.html) for a list).",
"isModifier": false,
"short": "Value of extension",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"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"
} ],
"max": "1",
"id": "Extension.extension:roc.value[x]",
"condition": [ "ext-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
}, {
"path": "Extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"isModifier": false,
"short": "identifies the meaning of the extension",
"fixedUri": "http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.quality",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "http://hl7.org/fhirpath/System.String",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
} ]
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"isSummary": false
}, {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"source": "http://hl7.org/fhir/StructureDefinition/Element|5.0.0",
"severity": "error",
"expression": "hasValue() or (children().count() > id.count())"
} ],
"path": "Extension.value[x]",
"min": 0,
"definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R5/extensibility.html) for a list).",
"isModifier": false,
"short": "Value of extension",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"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"
} ],
"max": "1",
"id": "Extension.value[x]",
"condition": [ "ext-1" ],
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"isSummary": false
} ],
"extension": [ {
"url": "http://hl7.org/fhir/tools/StructureDefinition/snapshot-base-version",
"valueString": "5.0.0"
} ]
},
"status": "active",
"id": "97c5ae21-636c-4388-8a56-206f5aada1a0",
"kind": "complex-type",
"url": "http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.quality",
"context": [ {
"type": "element",
"expression": "MolecularSequence"
} ],
"version": "0.0.1-snapshot-2",
"differential": {
"element": [ {
"id": "Extension",
"max": "*",
"min": 0,
"base": {
"max": "*",
"min": 0,
"path": "Extension"
},
"path": "Extension",
"short": "An set of value as quality of sequence",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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))."
}, {
"id": "Extension.extension",
"max": "*",
"min": 1,
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
},
"path": "Extension.extension",
"slicing": {
"rules": "closed",
"ordered": false,
"discriminator": [ {
"path": "url",
"type": "value"
} ]
}
}, {
"path": "Extension.extension",
"min": 1,
"definition": "INDEL / SNP / Undefined variant.",
"short": "indel | snp | unknown",
"sliceName": "type",
"max": "1",
"id": "Extension.extension:type",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:type.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "type"
}, {
"id": "Extension.extension:type.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "code"
} ],
"short": "indel | snp | unknown",
"binding": {
"strength": "required",
"valueSet": "http://hl7.org/fhir/4.0/ValueSet/R4-quality-type-for-R5|0.0.1-snapshot-2",
"description": "Type for quality report."
},
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "INDEL / SNP / Undefined variant."
}, {
"path": "Extension.extension",
"min": 0,
"definition": "Gold standard sequence used for comparing against.",
"short": "Standard sequence for comparison",
"sliceName": "standardSequence",
"max": "1",
"id": "Extension.extension:standardSequence",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:standardSequence.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "standardSequence"
}, {
"id": "Extension.extension:standardSequence.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "CodeableConcept"
} ],
"short": "Standard sequence for comparison",
"binding": {
"strength": "example",
"valueSet": "http://hl7.org/fhir/4.0/ValueSet/R4-sequence-quality-standardSequence-for-R5|0.0.1-snapshot-2",
"description": "Reference identifier of the sequence that used to mark the quality of tested samples."
},
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "Gold standard sequence used for comparing against."
}, {
"path": "Extension.extension",
"min": 0,
"definition": "Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"short": "Start position of the sequence",
"sliceName": "start",
"max": "1",
"id": "Extension.extension:start",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:start.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "start"
}, {
"id": "Extension.extension:start.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "integer"
} ],
"short": "Start position of the sequence",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive."
}, {
"path": "Extension.extension",
"min": 0,
"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.",
"short": "End position of the sequence",
"sliceName": "end",
"max": "1",
"id": "Extension.extension:end",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:end.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "end"
}, {
"id": "Extension.extension:end.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "integer"
} ],
"short": "End position of the sequence",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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."
}, {
"path": "Extension.extension",
"min": 0,
"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)).",
"short": "Quality score for the comparison",
"sliceName": "score",
"max": "1",
"id": "Extension.extension:score",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:score.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "score"
}, {
"id": "Extension.extension:score.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "Quantity"
} ],
"short": "Quality score for the comparison",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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))."
}, {
"path": "Extension.extension",
"min": 0,
"definition": "Which method is used to get sequence quality.",
"short": "Method to get quality",
"sliceName": "method",
"max": "1",
"id": "Extension.extension:method",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:method.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "method"
}, {
"id": "Extension.extension:method.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "CodeableConcept"
} ],
"short": "Method to get quality",
"binding": {
"strength": "example",
"valueSet": "http://hl7.org/fhir/4.0/ValueSet/R4-sequence-quality-method-for-R5|0.0.1-snapshot-2",
"description": "The method used to evaluate the numerical quality of the observed sequence."
},
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "Which method is used to get sequence quality."
}, {
"path": "Extension.extension",
"min": 0,
"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.",
"short": "True positives from the perspective of the truth data",
"sliceName": "truthTP",
"max": "1",
"id": "Extension.extension:truthTP",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:truthTP.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "truthTP"
}, {
"id": "Extension.extension:truthTP.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "decimal"
} ],
"short": "True positives from the perspective of the truth data",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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."
}, {
"path": "Extension.extension",
"min": 0,
"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.",
"short": "True positives from the perspective of the query data",
"sliceName": "queryTP",
"max": "1",
"id": "Extension.extension:queryTP",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:queryTP.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "queryTP"
}, {
"id": "Extension.extension:queryTP.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "decimal"
} ],
"short": "True positives from the perspective of the query data",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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."
}, {
"path": "Extension.extension",
"min": 0,
"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.",
"short": "False negatives",
"sliceName": "truthFN",
"max": "1",
"id": "Extension.extension:truthFN",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:truthFN.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "truthFN"
}, {
"id": "Extension.extension:truthFN.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "decimal"
} ],
"short": "False negatives",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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."
}, {
"path": "Extension.extension",
"min": 0,
"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.",
"short": "False positives",
"sliceName": "queryFP",
"max": "1",
"id": "Extension.extension:queryFP",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:queryFP.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "queryFP"
}, {
"id": "Extension.extension:queryFP.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "decimal"
} ],
"short": "False positives",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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."
}, {
"path": "Extension.extension",
"min": 0,
"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).",
"short": "False positives where the non-REF alleles in the Truth and Query Call Sets match",
"sliceName": "gtFP",
"max": "1",
"id": "Extension.extension:gtFP",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:gtFP.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "gtFP"
}, {
"id": "Extension.extension:gtFP.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "decimal"
} ],
"short": "False positives where the non-REF alleles in the Truth and Query Call Sets match",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"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)."
}, {
"path": "Extension.extension",
"min": 0,
"definition": "QUERY.TP / (QUERY.TP + QUERY.FP).",
"short": "Precision of comparison",
"sliceName": "precision",
"max": "1",
"id": "Extension.extension:precision",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:precision.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "precision"
}, {
"id": "Extension.extension:precision.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "decimal"
} ],
"short": "Precision of comparison",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "QUERY.TP / (QUERY.TP + QUERY.FP)."
}, {
"path": "Extension.extension",
"min": 0,
"definition": "TRUTH.TP / (TRUTH.TP + TRUTH.FN).",
"short": "Recall of comparison",
"sliceName": "recall",
"max": "1",
"id": "Extension.extension:recall",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:recall.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "recall"
}, {
"id": "Extension.extension:recall.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "decimal"
} ],
"short": "Recall of comparison",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "TRUTH.TP / (TRUTH.TP + TRUTH.FN)."
}, {
"path": "Extension.extension",
"min": 0,
"definition": "Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).",
"short": "F-score",
"sliceName": "fScore",
"max": "1",
"id": "Extension.extension:fScore",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:fScore.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "fScore"
}, {
"id": "Extension.extension:fScore.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.value[x]",
"type": [ {
"code": "decimal"
} ],
"short": "F-score",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall)."
}, {
"path": "Extension.extension",
"min": 0,
"definition": "Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.",
"short": "Receiver Operator Characteristic (ROC) Curve",
"sliceName": "roc",
"max": "1",
"id": "Extension.extension:roc",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:roc.extension",
"max": "*",
"min": 0,
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
},
"path": "Extension.extension.extension",
"slicing": {
"rules": "closed",
"ordered": false,
"discriminator": [ {
"path": "url",
"type": "value"
} ]
}
}, {
"path": "Extension.extension.extension",
"min": 0,
"definition": "Invidual data point representing the GQ (genotype quality) score threshold.",
"short": "Genotype quality score",
"sliceName": "score",
"max": "*",
"id": "Extension.extension:roc.extension:score",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:roc.extension:score.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.extension.url",
"fixedUri": "score"
}, {
"id": "Extension.extension:roc.extension:score.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.extension.value[x]",
"type": [ {
"code": "integer"
} ],
"short": "Genotype quality score",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "Invidual data point representing the GQ (genotype quality) score threshold."
}, {
"path": "Extension.extension.extension",
"min": 0,
"definition": "The number of true positives if the GQ score threshold was set to \"score\" field value.",
"short": "Roc score true positive numbers",
"sliceName": "numTP",
"max": "*",
"id": "Extension.extension:roc.extension:numTP",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:roc.extension:numTP.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.extension.url",
"fixedUri": "numTP"
}, {
"id": "Extension.extension:roc.extension:numTP.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.extension.value[x]",
"type": [ {
"code": "integer"
} ],
"short": "Roc score true positive numbers",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "The number of true positives if the GQ score threshold was set to \"score\" field value."
}, {
"path": "Extension.extension.extension",
"min": 0,
"definition": "The number of false positives if the GQ score threshold was set to \"score\" field value.",
"short": "Roc score false positive numbers",
"sliceName": "numFP",
"max": "*",
"id": "Extension.extension:roc.extension:numFP",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:roc.extension:numFP.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.extension.url",
"fixedUri": "numFP"
}, {
"id": "Extension.extension:roc.extension:numFP.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.extension.value[x]",
"type": [ {
"code": "integer"
} ],
"short": "Roc score false positive numbers",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "The number of false positives if the GQ score threshold was set to \"score\" field value."
}, {
"path": "Extension.extension.extension",
"min": 0,
"definition": "The number of false negatives if the GQ score threshold was set to \"score\" field value.",
"short": "Roc score false negative numbers",
"sliceName": "numFN",
"max": "*",
"id": "Extension.extension:roc.extension:numFN",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:roc.extension:numFN.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.extension.url",
"fixedUri": "numFN"
}, {
"id": "Extension.extension:roc.extension:numFN.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.extension.value[x]",
"type": [ {
"code": "integer"
} ],
"short": "Roc score false negative numbers",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "The number of false negatives if the GQ score threshold was set to \"score\" field value."
}, {
"path": "Extension.extension.extension",
"min": 0,
"definition": "Calculated precision if the GQ score threshold was set to \"score\" field value.",
"short": "Precision of the GQ score",
"sliceName": "precision",
"max": "*",
"id": "Extension.extension:roc.extension:precision",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:roc.extension:precision.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.extension.url",
"fixedUri": "precision"
}, {
"id": "Extension.extension:roc.extension:precision.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.extension.value[x]",
"type": [ {
"code": "decimal"
} ],
"short": "Precision of the GQ score",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "Calculated precision if the GQ score threshold was set to \"score\" field value."
}, {
"path": "Extension.extension.extension",
"min": 0,
"definition": "Calculated sensitivity if the GQ score threshold was set to \"score\" field value.",
"short": "Sensitivity of the GQ score",
"sliceName": "sensitivity",
"max": "*",
"id": "Extension.extension:roc.extension:sensitivity",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:roc.extension:sensitivity.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.extension.url",
"fixedUri": "sensitivity"
}, {
"id": "Extension.extension:roc.extension:sensitivity.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.extension.value[x]",
"type": [ {
"code": "decimal"
} ],
"short": "Sensitivity of the GQ score",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "Calculated sensitivity if the GQ score threshold was set to \"score\" field value."
}, {
"path": "Extension.extension.extension",
"min": 0,
"definition": "Calculated fScore if the GQ score threshold was set to \"score\" field value.",
"short": "FScore of the GQ score",
"sliceName": "fMeasure",
"max": "*",
"id": "Extension.extension:roc.extension:fMeasure",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"base": {
"max": "*",
"min": 0,
"path": "Extension.extension"
}
}, {
"id": "Extension.extension:roc.extension:fMeasure.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.extension.url",
"fixedUri": "fMeasure"
}, {
"id": "Extension.extension:roc.extension:fMeasure.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
},
"path": "Extension.extension.extension.value[x]",
"type": [ {
"code": "decimal"
} ],
"short": "FScore of the GQ score",
"comment": "`MolecularSequence.quality` has no related element in R5:MolecularSequence",
"definition": "Calculated fScore if the GQ score threshold was set to \"score\" field value."
}, {
"id": "Extension.extension:roc.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.extension.url",
"fixedUri": "roc"
}, {
"id": "Extension.url",
"max": "1",
"min": 1,
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
},
"path": "Extension.url",
"fixedUri": "http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.quality"
} ]
},
"contact": [ {
"name": "FHIR Infrastructure",
"telecom": [ {
"value": "http://www.hl7.org/Special/committees/fiwg",
"system": "url"
} ]
} ],
"baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension|5.0.0"
}