Package | hl7.fhir.uv.xver-r3.r5 |
Resource Type | StructureDefinition |
Id | ext-R3-Sequence.variant |
FHIR Version | R5 |
Source | http://hl7.org/fhir/uv/xver/https://simplifier.net/resolve?scope=hl7.fhir.uv.xver-r3.r5@0.0.1-snapshot-1&canonical=http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.variant |
URL | http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.variant |
Version | 0.0.1-snapshot-1 |
Status | draft |
Date | 2025-06-03T03:12:25.2345073+02:00 |
Name | ext_R3_Sequence_variant |
Title | Cross-version Extension for R3.Sequence.variant for use in FHIR R5 |
Realm | uv |
Authority | hl7 |
Description | This cross-version extension represents Sequence.variant from http://hl7.org/fhir/StructureDefinition/Sequence|3.0.2 for use in FHIR R5. |
Type | Extension |
Kind | complex-type |
No resources found
No resources found
No extension usage examples found
No narrative content found in resource
{ "resourceType": "StructureDefinition", "id": "ext-R3-Sequence.variant", "url": "http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.variant", "version": "0.0.1-snapshot-1", "name": "ext_R3_Sequence_variant", "title": "Cross-version Extension for R3.Sequence.variant for use in FHIR R5", "status": "draft", "experimental": false, "date": "2025-06-03T03:12:25.2345073+02:00", "description": "This cross-version extension represents Sequence.variant from http://hl7.org/fhir/StructureDefinition/Sequence|3.0.2 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", "min": 0, "max": "*", "base": { "path": "Extension", "min": 0, "max": "*" }, "constraint": [ { "key": "ele-1", "severity": "error", "human": "All FHIR elements must have a @value or children", "expression": "hasValue() or (children().count() > id.count())", "source": "http://hl7.org/fhir/StructureDefinition/Element" }, { "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, "mapping": [ { "identity": "rim", "map": "n/a,N/A" } ] }, { "id": "Extension.id", "path": "Extension.id", "representation": [ "xmlAttr" ], "short": "Unique id for inter-element referencing", "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", "min": 0, "max": "1", "base": { "path": "Element.id", "min": 0, "max": "1" }, "type": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl": "id" } ], "code": "http://hl7.org/fhirpath/System.String" } ], "condition": [ "ele-1" ], "isModifier": false, "isSummary": false, "mapping": [ { "identity": "rim", "map": "n/a" } ] }, { "id": "Extension.extension", "path": "Extension.extension", "slicing": { "discriminator": [ { "type": "value", "path": "url" } ], "description": "Extensions are always sliced by (at least) url", "ordered": false, "rules": "closed" }, "short": "Additional content defined by implementations", "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", "alias": [ "extensions", "user content" ], "min": 0, "max": "*", "base": { "path": "Element.extension", "min": 0, "max": "*" }, "type": [ { "code": "Extension" } ], "constraint": [ { "key": "ele-1", "severity": "error", "human": "All FHIR elements must have a @value or children", "expression": "hasValue() or (children().count() > id.count())", "source": "http://hl7.org/fhir/StructureDefinition/Element" }, { "key": "ext-1", "severity": "error", "human": "Must have either extensions or value[x], not both", "expression": "extension.exists() != value.exists()", "source": "http://hl7.org/fhir/StructureDefinition/Extension" } ], "isModifier": false, "isSummary": false, "mapping": [ { "identity": "rim", "map": "n/a" } ] }, { "id": "Extension.extension:start", "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", "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:start.id", "path": "Extension.extension.id", "representation": [ "xmlAttr" ], "short": "Unique id for inter-element referencing", "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", "min": 0, "max": "1", "base": { "path": "Element.id", "min": 0, "max": "1" }, "type": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl": "id" } ], "code": "http://hl7.org/fhirpath/System.String" } ], "condition": [ "ele-1" ], "isModifier": false, "isSummary": false, "mapping": [ { "identity": "rim", "map": "n/a" } ] }, { "id": "Extension.extension:start.extension", "path": "Extension.extension.extension", "slicing": { "discriminator": [ { "type": "value", "path": "url" } ], "description": "Extensions are always sliced by (at least) url", "rules": "open" }, "short": "Additional content defined by implementations", "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", "alias": [ "extensions", "user content" ], "min": 0, "max": "*", "base": { "path": "Element.extension", "min": 0, "max": "*" }, "type": [ { "code": "Extension" } ], "constraint": [ { "key": "ele-1", "severity": "error", "human": "All FHIR elements must have a @value or children", "expression": "hasValue() or (children().count() > id.count())", "source": "http://hl7.org/fhir/StructureDefinition/Element" }, { "key": "ext-1", "severity": "error", "human": "Must have either extensions or value[x], not both", "expression": "extension.exists() != value.exists()", "source": "http://hl7.org/fhir/StructureDefinition/Extension" } ], "isModifier": false, "isSummary": false, "mapping": [ { "identity": "rim", "map": "n/a" } ] }, { "id": "Extension.extension:start.url", "path": "Extension.extension.url", "representation": [ "xmlAttr" ], "short": "identifies the meaning of the extension", "definition": "Source of the definition for the extension code - a logical name or a URL.", "comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.", "min": 1, "max": "1", "base": { "path": "Extension.url", "min": 1, "max": "1" }, "type": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl": "uri" } ], "code": "http://hl7.org/fhirpath/System.String" } ], "fixedUri": "start", "isModifier": false, "isSummary": false, "mapping": [ { "identity": "rim", "map": "N/A" } ] }, { "id": "Extension.extension:start.value[x]", "path": "Extension.extension.value[x]", "short": "Start position of the 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", "base": { "path": "Extension.value[x]", "min": 0, "max": "1" }, "type": [ { "code": "integer" } ], "condition": [ "ext-1" ], "constraint": [ { "key": "ele-1", "severity": "error", "human": "All FHIR elements must have a @value or children", "expression": "hasValue() or (children().count() > id.count())", "source": "http://hl7.org/fhir/StructureDefinition/Element" } ], "isModifier": false, "isSummary": false, "mapping": [ { "identity": "rim", "map": "N/A" } ] }, { "id": "Extension.extension:end", "path": "Extension.extension", "sliceName": "end", "short": "End position of the 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 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", "alias": [ "extensions", "user content" ], "min": 0, "max": "1", "base": { "path": "Element.extension", "min": 0, "max": "*" }, "type": [ { "code": "Extension" } ], "constraint": [ { "key": "ele-1", "severity": "error", "human": "All FHIR elements must have a @value or children", "expression": "hasValue() or (children().count() > id.count())", "source": "http://hl7.org/fhir/StructureDefinition/Element" }, { "key": "ext-1", "severity": "error", "human": "Must have either extensions or value[x], not both", "expression": "extension.exists() != value.exists()", "source": "http://hl7.org/fhir/StructureDefinition/Extension" } ], "isModifier": false, "isSummary": false, "mapping": [ { "identity": "rim", "map": "n/a" } ] }, { "id": "Extension.extension:end.id", "path": "Extension.extension.id", "representation": [ "xmlAttr" ], "short": "Unique id for inter-element referencing", "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.", "min": 0, "max": "1", "base": { "path": "Element.id", "min": 0, "max": "1" }, "type": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl": "id" } ], "code": "http://hl7.org/fhirpath/System.String" } ], "condition": [ "ele-1" ], "isModifier": false, "isSummary": false, "mapping": [ { "identity": "rim", "map": "n/a" } ] }, { "id": "Extension.extension:end.extension", "path": "Extension.extension.extension", "slicing": { "discriminator": [ { "type": "value", "path": "url" } ], "description": "Extensions are always sliced by (at least) url", "rules": "open" }, "short": "Additional content defined by implementations", "definition": "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.", "comment": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.", "alias": [ "extensions", "user content" ], "min": 0, "max": "*", "base": { "path": "Element.extension", "min": 0, "max": "*" }, "type": [ { "code": "Extension" } ], "constraint": [ { "key": "ele-1", "severity": "error", "human": "All FHIR elements must have a @value or children", "expression": "hasValue() or (children().count() > id.count())", "source": "http://hl7.org/fhir/StructureDefinition/Element" }, { "key": "ext-1", "severity": "error", "human": "Must have either extensions or value[x], not both", "expression": "extension.exists() != value.exists()", "source": "http://hl7.org/fhir/StructureDefinition/Extension" } ], "isModifier": false, "isSummary": false, "mapping": [ { "identity": "rim", "map": "n/a" } ] }, { "id": "Extension.extension:end.url", "path": "Extension.extension.url", "representation": [ "xmlAttr" ], "short": "identifies the meaning of the extension", "definition": "Source of the definition for the extension code - a logical name or a URL.", "comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.", "min": 1, "max": "1", "base": { "path": "Extension.url", "min": 1, "max": "1" }, "type": [ { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl": "uri" } ], "code": "http://hl7.org/fhirpath/System.String" } ], "fixedUri": "end", "isModifier": false, "isSummary": false, "mapping": [ { "identity": "rim", "map": "N/A" } ] }, { "id": "Extension.extension:end.value[x]", "path": "Extension.extension.value[x]", "short": "End position of the 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 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", "base": { "path": "Extension.value[x]", "min": 0, "max": "1" }, "type": [ { "code": "integer" } ], "condition": [ "ext-1" ], "constraint": [ { "key": "ele-1", "severity": "error", "human": "All FHIR elements must have a @value or children", "expression": "hasValue() or (children().count() > id.count())", "source": "http://hl7.org/fhir/StructureDefinition/Element" } ], "isModifier": false, "isSummary": false, "mapping": [ { "identity": "rim", "map": "N/A" } ] }, { "id": "Extension.extension: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", "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:observedAllele.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:observedAllele.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:observedAllele.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": "observedAllele", "isModifier": false, "isSummary": false, "mapping": [ { "identity": "rim", "map": "N/A" } ] }, { "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/3.0/StructureDefinition/extension-Sequence.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 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 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/3.0/StructureDefinition/extension-Sequence.variant" } ] } }