| Package | hl7.fhir.uv.xver-r4b.r5 |
| Type | StructureDefinition |
| Id | Id |
| FHIR Version | R5 |
| Source | http://hl7.org/fhir/uv/xver/https://simplifier.net/resolve?scope=hl7.fhir.uv.xver-r4b.r5@0.0.1-snapshot-1&canonical=http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.variant |
| Url | http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.variant |
| Version | 0.0.1-snapshot-1 |
| Status | draft |
| Date | 2025-06-03T03:14:04.5804275+02:00 |
| Name | ext_R4B_MolecularSequence_variant |
| Title | Cross-version Extension for R4B.MolecularSequence.variant for use in FHIR R5 |
| Experimental | False |
| Realm | uv |
| Authority | hl7 |
| Description | This cross-version extension represents MolecularSequence.variant from http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.3.0 for use in FHIR R5. |
| Type | Extension |
| Kind | complex-type |
No resources found
No resources found
FHIR{
"resourceType" : "StructureDefinition",
"id" : "ext-R4B-MolecularSequence.variant",
"url" : "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.variant",
"version" : "0.0.1-snapshot-1",
"name" : "ext_R4B_MolecularSequence_variant",
"title" : "Cross-version Extension for R4B.MolecularSequence.variant for use in FHIR R5",
"status" : "draft",
"experimental" : false,
"date" : "2025-06-03T03:14:04.5804275+02:00",
"description" : "This cross-version extension represents MolecularSequence.variant from http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.3.0 for use in FHIR R5.",
"fhirVersion" : "5.0.0",
"kind" : "complex-type",
"abstract" : false,
"context" : [
{
"type" : "element",
"expression" : "MolecularSequence"
}
],
"type" : "Extension",
"baseDefinition" : "http://hl7.org/fhir/StructureDefinition/Extension",
"derivation" : "constraint",
"snapshot" : {
"element" : [
{
"id" : "Extension",
"path" : "Extension",
"short" : "Variant in sequence",
"definition" : "The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
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"comment" : "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
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"sliceName" : "start",
"short" : "Start position of the variant on the reference sequence",
"definition" : "Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
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"extensions",
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"comment" : "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
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"path" : "Extension.extension.url",
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"comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min" : 1,
"max" : "1",
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"path" : "Extension.url",
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"short" : "Start position of the variant on the reference sequence",
"definition" : "Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
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"definition" : "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
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"comment" : "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
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{
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]
},
{
"id" : "Extension.extension:observedAllele.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Allele that was observed",
"definition" : "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "string"
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:referenceAllele",
"path" : "Extension.extension",
"sliceName" : "referenceAllele",
"short" : "Allele in the reference sequence",
"definition" : "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"alias" : [
"extensions",
"user content"
],
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:referenceAllele.id",
"path" : "Extension.extension.id",
"representation" : [
"xmlAttr"
],
"short" : "Unique id for inter-element referencing",
"definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.id",
"min" : 0,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "id"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"condition" : [
"ele-1"
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:referenceAllele.extension",
"path" : "Extension.extension.extension",
"slicing" : {
"discriminator" : [
{
"type" : "value",
"path" : "url"
}
],
"description" : "Extensions are always sliced by (at least) url",
"rules" : "open"
},
"short" : "Additional content defined by implementations",
"definition" : "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment" : "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias" : [
"extensions",
"user content"
],
"min" : 0,
"max" : "*",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:referenceAllele.url",
"path" : "Extension.extension.url",
"representation" : [
"xmlAttr"
],
"short" : "identifies the meaning of the extension",
"definition" : "Source of the definition for the extension code - a logical name or a URL.",
"comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min" : 1,
"max" : "1",
"base" : {
"path" : "Extension.url",
"min" : 1,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "uri"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri" : "referenceAllele",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:referenceAllele.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Allele in the reference sequence",
"definition" : "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "string"
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:cigar",
"path" : "Extension.extension",
"sliceName" : "cigar",
"short" : "Extended CIGAR string for aligning the sequence with reference bases",
"definition" : "Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"alias" : [
"extensions",
"user content"
],
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:cigar.id",
"path" : "Extension.extension.id",
"representation" : [
"xmlAttr"
],
"short" : "Unique id for inter-element referencing",
"definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.id",
"min" : 0,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "id"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"condition" : [
"ele-1"
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:cigar.extension",
"path" : "Extension.extension.extension",
"slicing" : {
"discriminator" : [
{
"type" : "value",
"path" : "url"
}
],
"description" : "Extensions are always sliced by (at least) url",
"rules" : "open"
},
"short" : "Additional content defined by implementations",
"definition" : "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment" : "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias" : [
"extensions",
"user content"
],
"min" : 0,
"max" : "*",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:cigar.url",
"path" : "Extension.extension.url",
"representation" : [
"xmlAttr"
],
"short" : "identifies the meaning of the extension",
"definition" : "Source of the definition for the extension code - a logical name or a URL.",
"comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min" : 1,
"max" : "1",
"base" : {
"path" : "Extension.url",
"min" : 1,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "uri"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri" : "cigar",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:cigar.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Extended CIGAR string for aligning the sequence with reference bases",
"definition" : "Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "string"
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:variantPointer",
"path" : "Extension.extension",
"sliceName" : "variantPointer",
"short" : "Pointer to observed variant information",
"definition" : "A pointer to an Observation containing variant information.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"alias" : [
"extensions",
"user content"
],
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:variantPointer.id",
"path" : "Extension.extension.id",
"representation" : [
"xmlAttr"
],
"short" : "Unique id for inter-element referencing",
"definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Element.id",
"min" : 0,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "id"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"condition" : [
"ele-1"
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:variantPointer.extension",
"path" : "Extension.extension.extension",
"slicing" : {
"discriminator" : [
{
"type" : "value",
"path" : "url"
}
],
"description" : "Extensions are always sliced by (at least) url",
"rules" : "open"
},
"short" : "Additional content defined by implementations",
"definition" : "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"comment" : "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
"alias" : [
"extensions",
"user content"
],
"min" : 0,
"max" : "*",
"base" : {
"path" : "Element.extension",
"min" : 0,
"max" : "*"
},
"type" : [
{
"code" : "Extension"
}
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key" : "ext-1",
"severity" : "error",
"human" : "Must have either extensions or value[x], not both",
"expression" : "extension.exists() != value.exists()",
"source" : "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "n/a"
}
]
},
{
"id" : "Extension.extension:variantPointer.url",
"path" : "Extension.extension.url",
"representation" : [
"xmlAttr"
],
"short" : "identifies the meaning of the extension",
"definition" : "Source of the definition for the extension code - a logical name or a URL.",
"comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min" : 1,
"max" : "1",
"base" : {
"path" : "Extension.url",
"min" : 1,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "uri"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri" : "variantPointer",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.extension:variantPointer.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Pointer to observed variant information",
"definition" : "A pointer to an Observation containing variant information.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "Reference",
"targetProfile" : [
"http://hl7.org/fhir/StructureDefinition/Observation"
]
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.url",
"path" : "Extension.url",
"representation" : [
"xmlAttr"
],
"short" : "identifies the meaning of the extension",
"definition" : "Source of the definition for the extension code - a logical name or a URL.",
"comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min" : 1,
"max" : "1",
"base" : {
"path" : "Extension.url",
"min" : 1,
"max" : "1"
},
"type" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl" : "uri"
}
],
"code" : "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri" : "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.variant",
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
},
{
"id" : "Extension.value[x]",
"path" : "Extension.value[x]",
"short" : "Value of extension",
"definition" : "Value of extension - must be one of a constrained set of the data types (see [Extensibility](extensibility.html) for a list).",
"min" : 0,
"max" : "1",
"base" : {
"path" : "Extension.value[x]",
"min" : 0,
"max" : "1"
},
"type" : [
{
"code" : "base64Binary"
},
{
"code" : "boolean"
},
{
"code" : "canonical"
},
{
"code" : "code"
},
{
"code" : "date"
},
{
"code" : "dateTime"
},
{
"code" : "decimal"
},
{
"code" : "id"
},
{
"code" : "instant"
},
{
"code" : "integer"
},
{
"code" : "integer64"
},
{
"code" : "markdown"
},
{
"code" : "oid"
},
{
"code" : "positiveInt"
},
{
"code" : "string"
},
{
"code" : "time"
},
{
"code" : "unsignedInt"
},
{
"code" : "uri"
},
{
"code" : "url"
},
{
"code" : "uuid"
},
{
"code" : "Address"
},
{
"code" : "Age"
},
{
"code" : "Annotation"
},
{
"code" : "Attachment"
},
{
"code" : "CodeableConcept"
},
{
"code" : "CodeableReference"
},
{
"code" : "Coding"
},
{
"code" : "ContactPoint"
},
{
"code" : "Count"
},
{
"code" : "Distance"
},
{
"code" : "Duration"
},
{
"code" : "HumanName"
},
{
"code" : "Identifier"
},
{
"code" : "Money"
},
{
"code" : "Period"
},
{
"code" : "Quantity"
},
{
"code" : "Range"
},
{
"code" : "Ratio"
},
{
"code" : "RatioRange"
},
{
"code" : "Reference"
},
{
"code" : "SampledData"
},
{
"code" : "Signature"
},
{
"code" : "Timing"
},
{
"code" : "ContactDetail"
},
{
"code" : "DataRequirement"
},
{
"code" : "Expression"
},
{
"code" : "ParameterDefinition"
},
{
"code" : "RelatedArtifact"
},
{
"code" : "TriggerDefinition"
},
{
"code" : "UsageContext"
},
{
"code" : "Availability"
},
{
"code" : "ExtendedContactDetail"
},
{
"code" : "Dosage"
},
{
"code" : "Meta"
}
],
"condition" : [
"ext-1"
],
"constraint" : [
{
"key" : "ele-1",
"severity" : "error",
"human" : "All FHIR elements must have a @value or children",
"expression" : "hasValue() or (children().count() > id.count())",
"source" : "http://hl7.org/fhir/StructureDefinition/Element"
}
],
"isModifier" : false,
"isSummary" : false,
"mapping" : [
{
"identity" : "rim",
"map" : "N/A"
}
]
}
]
},
"differential" : {
"element" : [
{
"id" : "Extension",
"path" : "Extension",
"short" : "Variant in sequence",
"definition" : "The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "*",
"isModifier" : false
},
{
"id" : "Extension.extension",
"path" : "Extension.extension",
"slicing" : {
"discriminator" : [
{
"type" : "value",
"path" : "url"
}
],
"ordered" : false,
"rules" : "closed"
},
"min" : 0,
"max" : "*"
},
{
"id" : "Extension.extension:start",
"path" : "Extension.extension",
"sliceName" : "start",
"short" : "Start position of the variant on the reference sequence",
"definition" : "Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"id" : "Extension.extension:start.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Start position of the variant on the reference sequence",
"definition" : "Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "integer"
}
]
},
{
"id" : "Extension.extension:end",
"path" : "Extension.extension",
"sliceName" : "end",
"short" : "End position of the variant on the reference sequence",
"definition" : "End position of the variant on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"id" : "Extension.extension:end.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "End position of the variant on the reference sequence",
"definition" : "End position of the variant on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "integer"
}
]
},
{
"id" : "Extension.extension:observedAllele",
"path" : "Extension.extension",
"sliceName" : "observedAllele",
"short" : "Allele that was observed",
"definition" : "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"id" : "Extension.extension:observedAllele.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Allele that was observed",
"definition" : "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "string"
}
]
},
{
"id" : "Extension.extension:referenceAllele",
"path" : "Extension.extension",
"sliceName" : "referenceAllele",
"short" : "Allele in the reference sequence",
"definition" : "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"id" : "Extension.extension:referenceAllele.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Allele in the reference sequence",
"definition" : "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "string"
}
]
},
{
"id" : "Extension.extension:cigar",
"path" : "Extension.extension",
"sliceName" : "cigar",
"short" : "Extended CIGAR string for aligning the sequence with reference bases",
"definition" : "Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"id" : "Extension.extension:cigar.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Extended CIGAR string for aligning the sequence with reference bases",
"definition" : "Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "string"
}
]
},
{
"id" : "Extension.extension:variantPointer",
"path" : "Extension.extension",
"sliceName" : "variantPointer",
"short" : "Pointer to observed variant information",
"definition" : "A pointer to an Observation containing variant information.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"min" : 0,
"max" : "1",
"isModifier" : false
},
{
"id" : "Extension.extension:variantPointer.value[x]",
"path" : "Extension.extension.value[x]",
"short" : "Pointer to observed variant information",
"definition" : "A pointer to an Observation containing variant information.",
"comment" : "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
"base" : {
"path" : "Extension.value[x]"
},
"type" : [
{
"code" : "Reference",
"targetProfile" : [
"http://hl7.org/fhir/StructureDefinition/Observation"
]
}
]
},
{
"id" : "Extension.url",
"path" : "Extension.url",
"min" : 1,
"max" : "1",
"fixedUri" : "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.variant"
}
]
},
"text" : {
}
}
XIG built as of ??metadata-date??. Found ??metadata-resources?? resources in ??metadata-packages?? packages.