FHIR Cross-Version Extensions package for FHIR R5 from FHIR R4B
0.0.1-snapshot-2 - informative
FHIR Cross-Version Extensions package for FHIR R5 from FHIR R4B
0.0.1-snapshot-2 - informative
FHIR Cross-Version Extensions package for FHIR R5 from FHIR R4B - Version 0.0.1-snapshot-2. See the Directory of published versions
| Page standards status: Informative | Maturity Level: 0 |
Definitions for the ext-R4B-MolecularSequence.referenceSeq extension.
Guidance on how to interpret the contents of this table can be foundhere
| 0. Extension | |
| Definition | A sequence that is used as a reference to describe variants that are present in a sequence analyzed. |
| Short | A sequence used as reference |
| Comments |
|
| Control | 0..1 |
| 2. Extension.extension | |
| Control | 0..* |
| Slicing | This element introduces a set of slices on Extension.extension. The slices areUnordered and Closed, and can be differentiated using the following discriminators: |
| 4. Extension.extension:chromosome | |
| Slice Name | chromosome |
| Definition | Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication (SO:0000340). |
| Short | Chromosome containing genetic finding |
| Comments |
|
| Control | 0..1 |
| 6. Extension.extension:chromosome.url | |
| Control | 1..1 |
| Fixed Value | chromosome |
| 8. Extension.extension:chromosome.value[x] | |
| Definition | Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication (SO:0000340). |
| Short | Chromosome containing genetic finding |
| Comments |
|
| Binding | For example codes, see http://terminology.hl7.org/ValueSet/chromosome-human|0.2.0 (example to http://terminology.hl7.org/ValueSet/chromosome-human|0.2.0)The chromosome containing the genetic finding |
| Type | CodeableConcept |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| 10. Extension.extension:genomeBuild | |
| Slice Name | genomeBuild |
| Definition | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used. |
| Short | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' |
| Comments |
|
| Control | 0..1 |
| 12. Extension.extension:genomeBuild.url | |
| Control | 1..1 |
| Fixed Value | genomeBuild |
| 14. Extension.extension:genomeBuild.value[x] | |
| Definition | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used. |
| Short | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' |
| Comments |
|
| Type | string |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| 16. Extension.extension:orientation | |
| Slice Name | orientation |
| Definition | A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand. |
| Short | sense | antisense |
| Comments |
|
| Control | 0..1 |
| 18. Extension.extension:orientation.url | |
| Control | 1..1 |
| Fixed Value | orientation |
| 20. Extension.extension:orientation.value[x] | |
| Definition | A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand. |
| Short | sense | antisense |
| Comments |
|
| Binding | The codes SHALL be taken from OrientationType (required to http://hl7.org/fhir/ValueSet/orientation-type|5.0.0)Type for orientation |
| Type | code |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| 22. Extension.extension:referenceSeqId | |
| Slice Name | referenceSeqId |
| Definition | Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences. |
| Short | Reference identifier |
| Comments |
|
| Control | 0..1 |
| 24. Extension.extension:referenceSeqId.url | |
| Control | 1..1 |
| Fixed Value | referenceSeqId |
| 26. Extension.extension:referenceSeqId.value[x] | |
| Definition | Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences. |
| Short | Reference identifier |
| Comments |
|
| Binding | For example codes, see R4B_sequence_referenceSeq_for_R5 (0.0.1-snapshot-2) (example to http://hl7.org/fhir/4.3/ValueSet/R4B-sequence-referenceSeq-for-R5|0.0.1-snapshot-2)Reference identifier for reference sequence |
| Type | CodeableConcept |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| 28. Extension.extension:referenceSeqPointer | |
| Slice Name | referenceSeqPointer |
| Definition |
|
| Short | A pointer to another MolecularSequence entity as reference sequence |
| Control | 0..1 |
| 30. Extension.extension:referenceSeqPointer.url | |
| Control | 1..1 |
| Fixed Value | referenceSeqPointer |
| 32. Extension.extension:referenceSeqPointer.value[x] | |
| Definition |
|
| Short | A pointer to another MolecularSequence entity as reference sequence |
| Type | Reference |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| 34. Extension.extension:referenceSeqString | |
| Slice Name | referenceSeqString |
| Definition | A string like "ACGT". |
| Short | A string to represent reference sequence |
| Comments |
|
| Control | 0..1 |
| 36. Extension.extension:referenceSeqString.url | |
| Control | 1..1 |
| Fixed Value | referenceSeqString |
| 38. Extension.extension:referenceSeqString.value[x] | |
| Definition | A string like "ACGT". |
| Short | A string to represent reference sequence |
| Comments |
|
| Type | string |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| 40. Extension.extension:strand | |
| Slice Name | strand |
| Definition | An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. |
| Short | watson | crick |
| Comments |
|
| Control | 0..1 |
| 42. Extension.extension:strand.url | |
| Control | 1..1 |
| Fixed Value | strand |
| 44. Extension.extension:strand.value[x] | |
| Definition | An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. |
| Short | watson | crick |
| Comments |
|
| Binding | The codes SHALL be taken from StrandType (required to http://hl7.org/fhir/ValueSet/strand-type|5.0.0)Type for strand |
| Type | code |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| 46. Extension.extension:windowStart | |
| Slice Name | windowStart |
| Definition | Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive. |
| Short | Start position of the window on the reference sequence |
| Comments |
|
| Control | 0..1 |
| 48. Extension.extension:windowStart.url | |
| Control | 1..1 |
| Fixed Value | windowStart |
| 50. Extension.extension:windowStart.value[x] | |
| Definition | Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive. |
| Short | Start position of the window on the reference sequence |
| Comments |
|
| Type | integer |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| 52. Extension.extension:windowEnd | |
| Slice Name | windowEnd |
| Definition | End position of the window 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. |
| Short | End position of the window on the reference sequence |
| Comments |
|
| Control | 0..1 |
| 54. Extension.extension:windowEnd.url | |
| Control | 1..1 |
| Fixed Value | windowEnd |
| 56. Extension.extension:windowEnd.value[x] | |
| Definition | End position of the window 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. |
| Short | End position of the window on the reference sequence |
| Comments |
|
| Type | integer |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| 58. Extension.url | |
| Control | 1..1 |
| Fixed Value | http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.referenceSeq |
Guidance on how to interpret the contents of this table can be foundhere
| 0. Extension | |
| Definition | A sequence that is used as a reference to describe variants that are present in a sequence analyzed. Optional Extension Element - found in all resources. |
| Short | A sequence used as referenceOptional Extensions Element |
| Comments |
|
| Control | 0..1* |
| Is Modifier | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists())ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists()) |
| 2. Extension.extension | |
| Definition | An Extension 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. |
| Short | ExtensionAdditional content defined by implementations |
| Comments | 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. |
| Control | 0..* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Alternate Names | extensions, user content |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists())ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists()) |
| Slicing | This element introduces a set of slices on Extension.extension. The slices areUnordered and ClosedOpen, and can be differentiated using the following discriminators: |
| 4. Extension.extension:chromosome | |
| Slice Name | chromosome |
| Definition | Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication (SO:0000340). |
| Short | Chromosome containing genetic findingAdditional content defined by implementations |
| Comments |
|
| Control | 0..1* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists())ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists()) |
| 6. Extension.extension:chromosome.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | chromosome |
| 8. Extension.extension:chromosome.value[x] | |
| Definition | Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication (SO:0000340). Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). |
| Short | Chromosome containing genetic findingValue of extension |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Binding | For example codes, see For codes, see http://terminology.hl7.org/ValueSet/chromosome-human|0.2.0 (example to http://terminology.hl7.org/ValueSet/chromosome-human|0.2.0)The chromosome containing the genetic finding |
| Type | CodeableConcept, date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, RatioRange, Coding, SampledData, id, positiveInt, Distance, Availability, integer64, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, ExtendedContactDetail, ParameterDefinition, dateTime, code, string, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, Reference, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, CodeableReference, Signature, unsignedInt, time |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 10. Extension.extension:genomeBuild | |
| Slice Name | genomeBuild |
| Definition | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used. |
| Short | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'Additional content defined by implementations |
| Comments |
|
| Control | 0..1* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists())ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists()) |
| 12. Extension.extension:genomeBuild.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | genomeBuild |
| 14. Extension.extension:genomeBuild.value[x] | |
| Definition | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used. Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). |
| Short | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'Value of extension |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Type | string, date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, RatioRange, Coding, SampledData, id, positiveInt, Distance, Availability, integer64, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, ExtendedContactDetail, CodeableConcept, ParameterDefinition, dateTime, code, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, Reference, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, CodeableReference, Signature, unsignedInt, time |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 16. Extension.extension:orientation | |
| Slice Name | orientation |
| Definition | A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand. |
| Short | sense | antisenseAdditional content defined by implementations |
| Comments |
|
| Control | 0..1* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists())ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists()) |
| 18. Extension.extension:orientation.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | orientation |
| 20. Extension.extension:orientation.value[x] | |
| Definition | A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand. Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). |
| Short | sense | antisenseValue of extension |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Binding | The codes SHALL be taken from For codes, see OrientationType (required to http://hl7.org/fhir/ValueSet/orientation-type|5.0.0)Type for orientation |
| Type | code, date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, RatioRange, Coding, SampledData, id, positiveInt, Distance, Availability, integer64, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, ExtendedContactDetail, CodeableConcept, ParameterDefinition, dateTime, string, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, Reference, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, CodeableReference, Signature, unsignedInt, time |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 22. Extension.extension:referenceSeqId | |
| Slice Name | referenceSeqId |
| Definition | Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences. |
| Short | Reference identifierAdditional content defined by implementations |
| Comments |
|
| Control | 0..1* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists())ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists()) |
| 24. Extension.extension:referenceSeqId.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | referenceSeqId |
| 26. Extension.extension:referenceSeqId.value[x] | |
| Definition | Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences. Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). |
| Short | Reference identifierValue of extension |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Binding | For example codes, see For codes, see R4B_sequence_referenceSeq_for_R5 (0.0.1-snapshot-2) (example to http://hl7.org/fhir/4.3/ValueSet/R4B-sequence-referenceSeq-for-R5|0.0.1-snapshot-2)Reference identifier for reference sequence |
| Type | CodeableConcept, date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, RatioRange, Coding, SampledData, id, positiveInt, Distance, Availability, integer64, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, ExtendedContactDetail, ParameterDefinition, dateTime, code, string, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, Reference, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, CodeableReference, Signature, unsignedInt, time |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 28. Extension.extension:referenceSeqPointer | |
| Slice Name | referenceSeqPointer |
| Definition |
|
| Short | A pointer to another MolecularSequence entity as reference sequenceAdditional content defined by implementations |
| Control | 0..1* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists())ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists()) |
| 30. Extension.extension:referenceSeqPointer.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | referenceSeqPointer |
| 32. Extension.extension:referenceSeqPointer.value[x] | |
| Definition |
Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). |
| Short | A pointer to another MolecularSequence entity as reference sequenceValue of extension |
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Type | Reference, date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, RatioRange, Coding, SampledData, id, positiveInt, Distance, Availability, integer64, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, ExtendedContactDetail, CodeableConcept, ParameterDefinition, dateTime, code, string, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, CodeableReference, Signature, unsignedInt, time |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 34. Extension.extension:referenceSeqString | |
| Slice Name | referenceSeqString |
| Definition | A string like "ACGT". |
| Short | A string to represent reference sequenceAdditional content defined by implementations |
| Comments |
|
| Control | 0..1* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists())ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists()) |
| 36. Extension.extension:referenceSeqString.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | referenceSeqString |
| 38. Extension.extension:referenceSeqString.value[x] | |
| Definition | A string like "ACGT". Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). |
| Short | A string to represent reference sequenceValue of extension |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Type | string, date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, RatioRange, Coding, SampledData, id, positiveInt, Distance, Availability, integer64, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, ExtendedContactDetail, CodeableConcept, ParameterDefinition, dateTime, code, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, Reference, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, CodeableReference, Signature, unsignedInt, time |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 40. Extension.extension:strand | |
| Slice Name | strand |
| Definition | An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. |
| Short | watson | crickAdditional content defined by implementations |
| Comments |
|
| Control | 0..1* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists())ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists()) |
| 42. Extension.extension:strand.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | strand |
| 44. Extension.extension:strand.value[x] | |
| Definition | An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). |
| Short | watson | crickValue of extension |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Binding | The codes SHALL be taken from For codes, see StrandType (required to http://hl7.org/fhir/ValueSet/strand-type|5.0.0)Type for strand |
| Type | code, date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, RatioRange, Coding, SampledData, id, positiveInt, Distance, Availability, integer64, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, ExtendedContactDetail, CodeableConcept, ParameterDefinition, dateTime, string, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, Reference, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, CodeableReference, Signature, unsignedInt, time |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 46. Extension.extension:windowStart | |
| Slice Name | windowStart |
| Definition | Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive. |
| Short | Start position of the window on the reference sequenceAdditional content defined by implementations |
| Comments |
|
| Control | 0..1* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists())ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists()) |
| 48. Extension.extension:windowStart.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | windowStart |
| 50. Extension.extension:windowStart.value[x] | |
| Definition | Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive. Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). |
| Short | Start position of the window on the reference sequenceValue of extension |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Type | integer, date, Meta, Address, Attachment, Count, DataRequirement, Dosage, uuid, Identifier, RatioRange, Coding, SampledData, id, positiveInt, Distance, Availability, integer64, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, ExtendedContactDetail, CodeableConcept, ParameterDefinition, dateTime, code, string, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, Reference, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, CodeableReference, Signature, unsignedInt, time |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 52. Extension.extension:windowEnd | |
| Slice Name | windowEnd |
| Definition | End position of the window 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. |
| Short | End position of the window on the reference sequenceAdditional content defined by implementations |
| Comments |
|
| Control | 0..1* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists())ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists()) |
| 54. Extension.extension:windowEnd.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | windowEnd |
| 56. Extension.extension:windowEnd.value[x] | |
| Definition | End position of the window 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. Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). |
| Short | End position of the window on the reference sequenceValue of extension |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Type | integer, date, Meta, Address, Attachment, Count, DataRequirement, Dosage, uuid, Identifier, RatioRange, Coding, SampledData, id, positiveInt, Distance, Availability, integer64, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, ExtendedContactDetail, CodeableConcept, ParameterDefinition, dateTime, code, string, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, Reference, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, CodeableReference, Signature, unsignedInt, time |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 58. Extension.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.referenceSeq |
Guidance on how to interpret the contents of this table can be foundhere
| 0. Extension | |
| Definition | A sequence that is used as a reference to describe variants that are present in a sequence analyzed. |
| Short | A sequence used as reference |
| Comments |
|
| Control | 0..1 |
| Is Modifier | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| 2. Extension.id | |
| Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
| Short | Unique id for inter-element referencing |
| Control | 0..1 This element is affected by the following invariants: ele-1 |
| Type | id |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| 4. Extension.extension | |
| Definition | An Extension |
| Short | Extension |
| Control | 0..* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| Slicing | This element introduces a set of slices on Extension.extension. The slices areUnordered and Closed, and can be differentiated using the following discriminators: |
| 6. Extension.extension:chromosome | |
| Slice Name | chromosome |
| Definition | Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication (SO:0000340). |
| Short | Chromosome containing genetic finding |
| Comments |
|
| Control | 0..1 |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| 8. Extension.extension:chromosome.id | |
| Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
| Short | Unique id for inter-element referencing |
| Control | 0..1 This element is affected by the following invariants: ele-1 |
| Type | id |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| 10. Extension.extension:chromosome.extension | |
| 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. |
| Short | Additional content defined by implementations |
| Comments | 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. |
| Control | 0..* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Alternate Names | extensions, user content |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| Slicing | This element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators: |
| 12. Extension.extension:chromosome.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | chromosome |
| 14. Extension.extension:chromosome.value[x] | |
| Definition | Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication (SO:0000340). |
| Short | Chromosome containing genetic finding |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Binding | For example codes, see http://terminology.hl7.org/ValueSet/chromosome-human|0.2.0 (example to http://terminology.hl7.org/ValueSet/chromosome-human|0.2.0)The chromosome containing the genetic finding |
| Type | CodeableConcept |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 16. Extension.extension:genomeBuild | |
| Slice Name | genomeBuild |
| Definition | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used. |
| Short | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' |
| Comments |
|
| Control | 0..1 |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| 18. Extension.extension:genomeBuild.id | |
| Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
| Short | Unique id for inter-element referencing |
| Control | 0..1 This element is affected by the following invariants: ele-1 |
| Type | id |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| 20. Extension.extension:genomeBuild.extension | |
| 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. |
| Short | Additional content defined by implementations |
| Comments | 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. |
| Control | 0..* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Alternate Names | extensions, user content |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| Slicing | This element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators: |
| 22. Extension.extension:genomeBuild.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | genomeBuild |
| 24. Extension.extension:genomeBuild.value[x] | |
| Definition | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used. |
| Short | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Type | string |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 26. Extension.extension:orientation | |
| Slice Name | orientation |
| Definition | A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand. |
| Short | sense | antisense |
| Comments |
|
| Control | 0..1 |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| 28. Extension.extension:orientation.id | |
| Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
| Short | Unique id for inter-element referencing |
| Control | 0..1 This element is affected by the following invariants: ele-1 |
| Type | id |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| 30. Extension.extension:orientation.extension | |
| 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. |
| Short | Additional content defined by implementations |
| Comments | 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. |
| Control | 0..* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Alternate Names | extensions, user content |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| Slicing | This element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators: |
| 32. Extension.extension:orientation.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | orientation |
| 34. Extension.extension:orientation.value[x] | |
| Definition | A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand. |
| Short | sense | antisense |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Binding | The codes SHALL be taken from OrientationType (required to http://hl7.org/fhir/ValueSet/orientation-type|5.0.0)Type for orientation |
| Type | code |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 36. Extension.extension:referenceSeqId | |
| Slice Name | referenceSeqId |
| Definition | Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences. |
| Short | Reference identifier |
| Comments |
|
| Control | 0..1 |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| 38. Extension.extension:referenceSeqId.id | |
| Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
| Short | Unique id for inter-element referencing |
| Control | 0..1 This element is affected by the following invariants: ele-1 |
| Type | id |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| 40. Extension.extension:referenceSeqId.extension | |
| 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. |
| Short | Additional content defined by implementations |
| Comments | 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. |
| Control | 0..* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Alternate Names | extensions, user content |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| Slicing | This element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators: |
| 42. Extension.extension:referenceSeqId.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | referenceSeqId |
| 44. Extension.extension:referenceSeqId.value[x] | |
| Definition | Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences. |
| Short | Reference identifier |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Binding | For example codes, see R4B_sequence_referenceSeq_for_R5 (0.0.1-snapshot-2) (example to http://hl7.org/fhir/4.3/ValueSet/R4B-sequence-referenceSeq-for-R5|0.0.1-snapshot-2)Reference identifier for reference sequence |
| Type | CodeableConcept |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 46. Extension.extension:referenceSeqPointer | |
| Slice Name | referenceSeqPointer |
| Definition |
|
| Short | A pointer to another MolecularSequence entity as reference sequence |
| Control | 0..1 |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| 48. Extension.extension:referenceSeqPointer.id | |
| Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
| Short | Unique id for inter-element referencing |
| Control | 0..1 This element is affected by the following invariants: ele-1 |
| Type | id |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| 50. Extension.extension:referenceSeqPointer.extension | |
| 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. |
| Short | Additional content defined by implementations |
| Comments | 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. |
| Control | 0..* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Alternate Names | extensions, user content |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| Slicing | This element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators: |
| 52. Extension.extension:referenceSeqPointer.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | referenceSeqPointer |
| 54. Extension.extension:referenceSeqPointer.value[x] | |
| Definition |
|
| Short | A pointer to another MolecularSequence entity as reference sequence |
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Type | Reference |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 56. Extension.extension:referenceSeqString | |
| Slice Name | referenceSeqString |
| Definition | A string like "ACGT". |
| Short | A string to represent reference sequence |
| Comments |
|
| Control | 0..1 |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| 58. Extension.extension:referenceSeqString.id | |
| Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
| Short | Unique id for inter-element referencing |
| Control | 0..1 This element is affected by the following invariants: ele-1 |
| Type | id |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| 60. Extension.extension:referenceSeqString.extension | |
| 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. |
| Short | Additional content defined by implementations |
| Comments | 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. |
| Control | 0..* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Alternate Names | extensions, user content |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| Slicing | This element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators: |
| 62. Extension.extension:referenceSeqString.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | referenceSeqString |
| 64. Extension.extension:referenceSeqString.value[x] | |
| Definition | A string like "ACGT". |
| Short | A string to represent reference sequence |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Type | string |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 66. Extension.extension:strand | |
| Slice Name | strand |
| Definition | An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. |
| Short | watson | crick |
| Comments |
|
| Control | 0..1 |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| 68. Extension.extension:strand.id | |
| Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
| Short | Unique id for inter-element referencing |
| Control | 0..1 This element is affected by the following invariants: ele-1 |
| Type | id |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| 70. Extension.extension:strand.extension | |
| 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. |
| Short | Additional content defined by implementations |
| Comments | 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. |
| Control | 0..* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Alternate Names | extensions, user content |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| Slicing | This element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators: |
| 72. Extension.extension:strand.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | strand |
| 74. Extension.extension:strand.value[x] | |
| Definition | An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. |
| Short | watson | crick |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Binding | The codes SHALL be taken from StrandType (required to http://hl7.org/fhir/ValueSet/strand-type|5.0.0)Type for strand |
| Type | code |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 76. Extension.extension:windowStart | |
| Slice Name | windowStart |
| Definition | Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive. |
| Short | Start position of the window on the reference sequence |
| Comments |
|
| Control | 0..1 |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| 78. Extension.extension:windowStart.id | |
| Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
| Short | Unique id for inter-element referencing |
| Control | 0..1 This element is affected by the following invariants: ele-1 |
| Type | id |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| 80. Extension.extension:windowStart.extension | |
| 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. |
| Short | Additional content defined by implementations |
| Comments | 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. |
| Control | 0..* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Alternate Names | extensions, user content |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| Slicing | This element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators: |
| 82. Extension.extension:windowStart.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | windowStart |
| 84. Extension.extension:windowStart.value[x] | |
| Definition | Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive. |
| Short | Start position of the window on the reference sequence |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Type | integer |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 86. Extension.extension:windowEnd | |
| Slice Name | windowEnd |
| Definition | End position of the window 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. |
| Short | End position of the window on the reference sequence |
| Comments |
|
| Control | 0..1 |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| 88. Extension.extension:windowEnd.id | |
| Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
| Short | Unique id for inter-element referencing |
| Control | 0..1 This element is affected by the following invariants: ele-1 |
| Type | id |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| 90. Extension.extension:windowEnd.extension | |
| 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. |
| Short | Additional content defined by implementations |
| Comments | 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. |
| Control | 0..* |
| Type | Extension |
| Is Modifier | false |
| Summary | false |
| Alternate Names | extensions, user content |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))ext-1: Must have either extensions or value[x], not both ( extension.exists() != value.exists()) |
| Slicing | This element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators: |
| 92. Extension.extension:windowEnd.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | windowEnd |
| 94. Extension.extension:windowEnd.value[x] | |
| Definition | End position of the window 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. |
| Short | End position of the window on the reference sequence |
| Comments |
|
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Type | integer |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
| 96. Extension.url | |
| Definition | Source of the definition for the extension code - a logical name or a URL. |
| Short | identifies the meaning of the extension |
| Comments | 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. |
| Control | 1..1 |
| Type | uri |
| Is Modifier | false |
| XML Format | In the XML format, this property is represented as an attribute. |
| Summary | false |
| Fixed Value | http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.referenceSeq |
| 98. Extension.value[x] | |
| Definition | Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). |
| Short | Value of extension |
| Control | 0..1 This element is affected by the following invariants: ext-1 |
| Type | Choice of: base64Binary, boolean, canonical, code, date, dateTime, decimal, id, instant, integer, integer64, markdown, oid, positiveInt, string, time, unsignedInt, uri, url, uuid, Address, Age, Annotation, Attachment, CodeableConcept, CodeableReference, Coding, ContactPoint, Count, Distance, Duration, HumanName, Identifier, Money, Period, Quantity, Range, Ratio, RatioRange, Reference, SampledData, Signature, Timing, ContactDetail, DataRequirement, Expression, ParameterDefinition, RelatedArtifact, TriggerDefinition, UsageContext, Availability, ExtendedContactDetail, Dosage, Meta |
| [x] Note | SeeChoice of Data Typesfor further information about how to use [x] |
| Is Modifier | false |
| Primitive Value | This primitive element may be present, or absent, or replaced by an extension |
| Summary | false |
| Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) |
IG © 2025+ FHIR Infrastructure. Package hl7.fhir.uv.xver-r4b.r5#0.0.1-snapshot-2 based on FHIR 5.0.0. Generated 2025-09-13
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