Molecular Definition Implementation Guide for Molecular Data Types
1.0.0-ballot1 - ci-build
Molecular Definition Implementation Guide for Molecular Data Types, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 1.0.0-ballot1 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/molecular-definition-data-types/ and changes regularly. See the Directory of published versions
Official URL: http://hl7.org/fhir/uv/molecular-definition-data-types/StructureDefinition/sequence | Version: 1.0.0-ballot1 | |||
Standards status: Informative | Computable Name: Sequence |
Sequence profile of MolecularDefinition
The Sequence profile serves as a foundational component of this implementation guide, designed to represent raw genetic sequences such as DNA, RNA, and proteins. It supports multiple formats to accommodate diverse implementation needs. Unlike Allele and Variation profiles that emphasize genomic location, the Sequence profile focuses on the intrinsic composition of the genetic sequence. Additionally, it plays a crucial role in integrating with other profiles within this guide, enhancing their functionality.
Usages:
You can also check for usages in the FHIR IG Statistics
Description of Profiles, Differentials, Snapshots and how the different presentations work.
Name | Flags | Card. | Type | Description & Constraints Filter: ![]() ![]() |
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0..* | MolecularDefinition | Definitional content for a molecular entity | |
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?!Σ | 0..1 | uri | A set of rules under which this content was created |
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0..* | Resource | Contained, inline Resources | |
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?!Σ | 0..* | Extension | Extensions that cannot be ignored |
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SΣ | 1..1 | CodeableConcept | Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type (required) |
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Σ | 0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology (required) |
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Path | Conformance | ValueSet | URI |
MolecularDefinition.type | required | MoleculeTypeVS(a valid code from Molecule Type)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type From this IG | |
MolecularDefinition.topology | required | TopologyVS(a valid code from Topology)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology From this IG |
Id | Grade | Path(s) | Details | Requirements |
dom-2 | error | MolecularDefinition | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
dom-3 | error | MolecularDefinition | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty() | |
dom-4 | error | MolecularDefinition | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
dom-5 | error | MolecularDefinition | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
dom-6 | best practice | MolecularDefinition | A resource should have narrative for robust management : text.`div`.exists() | |
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) |
This structure is derived from MolecularDefinition
Path | Conformance | ValueSet | URI |
MolecularDefinition.type | required | MoleculeTypeVS(a valid code from Molecule Type)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type From this IG | |
MolecularDefinition.topology | required | TopologyVS(a valid code from Topology)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology From this IG | |
MolecularDefinition.representation.literal.encoding | required | EncodingsVS(a valid code from Encodings)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/encodings From this IG | |
MolecularDefinition.representation.literal.value | extensible |
|
Name | Flags | Card. | Type | Description & Constraints Filter: ![]() ![]() | ||||||||||||||||||
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0..* | MolecularDefinition | Definitional content for a molecular entity | |||||||||||||||||||
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Σ | 0..1 | id | Logical id of this artifact | ||||||||||||||||||
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Σ | 0..1 | Meta | Metadata about the resource | ||||||||||||||||||
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?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||||||||||||||||
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0..1 | code | Language of the resource content Binding: AllLanguages (required): IETF language tag for a human language
| |||||||||||||||||||
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0..1 | Narrative | Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements | |||||||||||||||||||
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0..* | Resource | Contained, inline Resources | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored | ||||||||||||||||||
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Σ | 0..* | Identifier | Unique ID of an instance | ||||||||||||||||||
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0..1 | markdown | Description of the Molecular Definition instance | |||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The type of molecule (e.g., DNA, RNA, amino acid) | ||||||||||||||||||
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SΣ | 1..1 | CodeableConcept | Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type (required) | ||||||||||||||||||
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Σ | 0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology (required) | ||||||||||||||||||
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Σ | 0..* | BackboneElement | A representation of a molecular entity | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The domain concept that is the focus of a given instance of the representation | ||||||||||||||||||
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Σ | 0..* | CodeableConcept | A code (e.g., sequence accession number) used to represent a molecular entity | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | A molecular entity defined as a string literal | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The encoding used in the value Binding: Molecular Definition Encodings (required) | ||||||||||||||||||
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Σ | 1..1 | string | A string literal representation of the molecular entity, using the encoding specified in encoding Binding Description: (extensible) ⚠: Refer to the addtional bindings for the literal encoding.
| ||||||||||||||||||
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Σ | 0..1 | Reference(DocumentReference) | A resolvable representation of a molecular entity (e.g., URI, attached and formatted file) | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | A molecular entity that is represented as a portion of a different entity | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 1..1 | Reference(MolecularDefinition) | The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | The interval on startingMolecule that defines the portion to be extracted to produce the intended entity | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | The coordinate system used to define the location | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system. | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The location of the origin of the coordinate system | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The normalization method used for determining a location within the coordinate system | ||||||||||||||||||
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Σ | 0..1 | The start location of the interval | |||||||||||||||||||
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Quantity | |||||||||||||||||||||
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Range | |||||||||||||||||||||
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Σ | 0..1 | The end location of the interval | |||||||||||||||||||
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Quantity | |||||||||||||||||||||
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Range | |||||||||||||||||||||
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Σ | 0..1 | boolean | A flag that indicates whether the extracted sequence should be reverse complemented | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | A representation as a repeated motif | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 1..1 | Reference(MolecularDefinition) | The motif that is repeated | ||||||||||||||||||
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Σ | 1..1 | integer | The number of copies of the motif | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | An ordered concatenation of molecular entities | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 1..* | BackboneElement | One of the concatenated entities | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 1..1 | Reference(MolecularDefinition) | A reference to the sequence that defines this specific concatenated element | ||||||||||||||||||
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Σ | 1..1 | integer | The ordinal index of the element within the concatenated representation | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | A molecular entity represented as an ordered series of edits on a specified starting entity | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 1..1 | Reference(MolecularDefinition) | The molecular entity on which edits will be applied | ||||||||||||||||||
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Σ | 0..* | BackboneElement | A defined edit (change) to be applied | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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0..1 | integer | Defines the order of edits when multiple edits are to be applied to the startingMolecule | |||||||||||||||||||
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Σ | 0..1 | BackboneElement | The interval on startingMolecule that defines the portion to be extracted to produce the intended entity | ||||||||||||||||||
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Σ | 0..1 | BackboneElement | The coordinate system used to define the location | ||||||||||||||||||
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system. | ||||||||||||||||||
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Σ | 0..1 | CodeableConcept | The location of the origin of the coordinate system | ||||||||||||||||||
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Σ | 0..1 | CodeableConcept | The normalization method used for determining a location within the coordinate system | ||||||||||||||||||
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Σ | 0..1 | The start location of the interval | |||||||||||||||||||
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Quantity | |||||||||||||||||||||
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Range | |||||||||||||||||||||
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Σ | 0..1 | The end location of the interval | |||||||||||||||||||
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Quantity | |||||||||||||||||||||
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Range | |||||||||||||||||||||
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Σ | 1..1 | Reference(MolecularDefinition) | The molecular entity that serves as the replacement in the edit operation | ||||||||||||||||||
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Σ | 0..1 | Reference(MolecularDefinition) | The portion of the molecular entity that is replaced by the replacementMolecule | ||||||||||||||||||
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Path | Conformance | ValueSet | URI |
MolecularDefinition.language | required | AllLanguageshttp://hl7.org/fhir/ValueSet/all-languages|6.0.0-ballot3 From the FHIR Standard | |
MolecularDefinition.type | required | MoleculeTypeVS(a valid code from Molecule Type)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type From this IG | |
MolecularDefinition.topology | required | TopologyVS(a valid code from Topology)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology From this IG | |
MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.system | extensible | LOINC LL5323-2http://loinc.org/vs/LL5323-2 | |
MolecularDefinition.representation.literal.encoding | required | EncodingsVS(a valid code from Encodings)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/encodings From this IG | |
MolecularDefinition.representation.literal.value | extensible | ||
MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem.system | extensible | LOINC LL5323-2http://loinc.org/vs/LL5323-2 | |
MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem.system | extensible | LOINC LL5323-2http://loinc.org/vs/LL5323-2 |
Id | Grade | Path(s) | Details | Requirements |
dom-2 | error | MolecularDefinition | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
dom-3 | error | MolecularDefinition | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty() | |
dom-4 | error | MolecularDefinition | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
dom-5 | error | MolecularDefinition | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
dom-6 | best practice | MolecularDefinition | A resource should have narrative for robust management : text.`div`.exists() | |
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) |
This structure is derived from MolecularDefinition
Key Elements View
Name | Flags | Card. | Type | Description & Constraints Filter: ![]() ![]() |
---|---|---|---|---|
![]() ![]() |
0..* | MolecularDefinition | Definitional content for a molecular entity | |
![]() ![]() ![]() |
?!Σ | 0..1 | uri | A set of rules under which this content was created |
![]() ![]() ![]() |
0..* | Resource | Contained, inline Resources | |
![]() ![]() ![]() |
?!Σ | 0..* | Extension | Extensions that cannot be ignored |
![]() ![]() ![]() |
SΣ | 1..1 | CodeableConcept | Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type (required) |
![]() ![]() ![]() |
Σ | 0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology (required) |
![]() |
Path | Conformance | ValueSet | URI |
MolecularDefinition.type | required | MoleculeTypeVS(a valid code from Molecule Type)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type From this IG | |
MolecularDefinition.topology | required | TopologyVS(a valid code from Topology)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology From this IG |
Id | Grade | Path(s) | Details | Requirements |
dom-2 | error | MolecularDefinition | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
dom-3 | error | MolecularDefinition | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty() | |
dom-4 | error | MolecularDefinition | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
dom-5 | error | MolecularDefinition | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
dom-6 | best practice | MolecularDefinition | A resource should have narrative for robust management : text.`div`.exists() | |
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) |
Differential View
This structure is derived from MolecularDefinition
Name | Flags | Card. | Type | Description & Constraints Filter: ![]() ![]() | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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0..* | MolecularDefinition | Definitional content for a molecular entity | |||||||||||||||||||
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S | 1..1 | CodeableConcept | Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type (required) | ||||||||||||||||||
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0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology (required) | |||||||||||||||||||
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0..0 | |||||||||||||||||||||
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0..0 | |||||||||||||||||||||
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0..1 | CodeableConcept | The encoding used in the value Binding: Molecular Definition Encodings (required) | |||||||||||||||||||
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1..1 | string | A string literal representation of the molecular entity, using the encoding specified in encoding Binding Description: (extensible) ⚠: Refer to the addtional bindings for the literal encoding.
| |||||||||||||||||||
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Path | Conformance | ValueSet | URI |
MolecularDefinition.type | required | MoleculeTypeVS(a valid code from Molecule Type)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type From this IG | |
MolecularDefinition.topology | required | TopologyVS(a valid code from Topology)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology From this IG | |
MolecularDefinition.representation.literal.encoding | required | EncodingsVS(a valid code from Encodings)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/encodings From this IG | |
MolecularDefinition.representation.literal.value | extensible |
|
Snapshot View
Name | Flags | Card. | Type | Description & Constraints Filter: ![]() ![]() | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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0..* | MolecularDefinition | Definitional content for a molecular entity | |||||||||||||||||||
![]() ![]() ![]() |
Σ | 0..1 | id | Logical id of this artifact | ||||||||||||||||||
![]() ![]() ![]() |
Σ | 0..1 | Meta | Metadata about the resource | ||||||||||||||||||
![]() ![]() ![]() |
?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||||||||||||||||
![]() ![]() ![]() |
0..1 | code | Language of the resource content Binding: AllLanguages (required): IETF language tag for a human language
| |||||||||||||||||||
![]() ![]() ![]() |
0..1 | Narrative | Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements | |||||||||||||||||||
![]() ![]() ![]() |
0..* | Resource | Contained, inline Resources | |||||||||||||||||||
![]() ![]() ![]() |
0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
![]() ![]() ![]() |
?!Σ | 0..* | Extension | Extensions that cannot be ignored | ||||||||||||||||||
![]() ![]() ![]() |
Σ | 0..* | Identifier | Unique ID of an instance | ||||||||||||||||||
![]() ![]() ![]() |
0..1 | markdown | Description of the Molecular Definition instance | |||||||||||||||||||
![]() ![]() ![]() |
Σ | 0..1 | CodeableConcept | The type of molecule (e.g., DNA, RNA, amino acid) | ||||||||||||||||||
![]() ![]() ![]() |
SΣ | 1..1 | CodeableConcept | Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type (required) | ||||||||||||||||||
![]() ![]() ![]() |
Σ | 0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology (required) | ||||||||||||||||||
![]() ![]() ![]() |
Σ | 0..* | BackboneElement | A representation of a molecular entity | ||||||||||||||||||
![]() ![]() ![]() ![]() |
0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The domain concept that is the focus of a given instance of the representation | ||||||||||||||||||
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Σ | 0..* | CodeableConcept | A code (e.g., sequence accession number) used to represent a molecular entity | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | A molecular entity defined as a string literal | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The encoding used in the value Binding: Molecular Definition Encodings (required) | ||||||||||||||||||
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Σ | 1..1 | string | A string literal representation of the molecular entity, using the encoding specified in encoding Binding Description: (extensible) ⚠: Refer to the addtional bindings for the literal encoding.
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Σ | 0..1 | Reference(DocumentReference) | A resolvable representation of a molecular entity (e.g., URI, attached and formatted file) | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | A molecular entity that is represented as a portion of a different entity | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 1..1 | Reference(MolecularDefinition) | The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | The interval on startingMolecule that defines the portion to be extracted to produce the intended entity | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | The coordinate system used to define the location | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system. | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The location of the origin of the coordinate system | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The normalization method used for determining a location within the coordinate system | ||||||||||||||||||
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Σ | 0..1 | The start location of the interval | |||||||||||||||||||
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Quantity | |||||||||||||||||||||
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Range | |||||||||||||||||||||
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Σ | 0..1 | The end location of the interval | |||||||||||||||||||
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Quantity | |||||||||||||||||||||
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Range | |||||||||||||||||||||
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Σ | 0..1 | boolean | A flag that indicates whether the extracted sequence should be reverse complemented | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | A representation as a repeated motif | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 1..1 | Reference(MolecularDefinition) | The motif that is repeated | ||||||||||||||||||
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Σ | 1..1 | integer | The number of copies of the motif | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | An ordered concatenation of molecular entities | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 1..* | BackboneElement | One of the concatenated entities | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 1..1 | Reference(MolecularDefinition) | A reference to the sequence that defines this specific concatenated element | ||||||||||||||||||
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Σ | 1..1 | integer | The ordinal index of the element within the concatenated representation | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | A molecular entity represented as an ordered series of edits on a specified starting entity | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 1..1 | Reference(MolecularDefinition) | The molecular entity on which edits will be applied | ||||||||||||||||||
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Σ | 0..* | BackboneElement | A defined edit (change) to be applied | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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0..1 | integer | Defines the order of edits when multiple edits are to be applied to the startingMolecule | |||||||||||||||||||
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Σ | 0..1 | BackboneElement | The interval on startingMolecule that defines the portion to be extracted to produce the intended entity | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 0..1 | BackboneElement | The coordinate system used to define the location | ||||||||||||||||||
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0..1 | string | Unique id for inter-element referencing | |||||||||||||||||||
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0..* | Extension | Additional content defined by implementations | |||||||||||||||||||
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?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system. | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The location of the origin of the coordinate system | ||||||||||||||||||
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Σ | 0..1 | CodeableConcept | The normalization method used for determining a location within the coordinate system | ||||||||||||||||||
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Σ | 0..1 | The start location of the interval | |||||||||||||||||||
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Quantity | |||||||||||||||||||||
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Range | |||||||||||||||||||||
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Σ | 0..1 | The end location of the interval | |||||||||||||||||||
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Quantity | |||||||||||||||||||||
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Range | |||||||||||||||||||||
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Σ | 1..1 | Reference(MolecularDefinition) | The molecular entity that serves as the replacement in the edit operation | ||||||||||||||||||
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Σ | 0..1 | Reference(MolecularDefinition) | The portion of the molecular entity that is replaced by the replacementMolecule | ||||||||||||||||||
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Path | Conformance | ValueSet | URI |
MolecularDefinition.language | required | AllLanguageshttp://hl7.org/fhir/ValueSet/all-languages|6.0.0-ballot3 From the FHIR Standard | |
MolecularDefinition.type | required | MoleculeTypeVS(a valid code from Molecule Type)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type From this IG | |
MolecularDefinition.topology | required | TopologyVS(a valid code from Topology)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology From this IG | |
MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.system | extensible | LOINC LL5323-2http://loinc.org/vs/LL5323-2 | |
MolecularDefinition.representation.literal.encoding | required | EncodingsVS(a valid code from Encodings)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/encodings From this IG | |
MolecularDefinition.representation.literal.value | extensible | ||
MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem.system | extensible | LOINC LL5323-2http://loinc.org/vs/LL5323-2 | |
MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem.system | extensible | LOINC LL5323-2http://loinc.org/vs/LL5323-2 |
Id | Grade | Path(s) | Details | Requirements |
dom-2 | error | MolecularDefinition | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
dom-3 | error | MolecularDefinition | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty() | |
dom-4 | error | MolecularDefinition | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
dom-5 | error | MolecularDefinition | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
dom-6 | best practice | MolecularDefinition | A resource should have narrative for robust management : text.`div`.exists() | |
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) |
This structure is derived from MolecularDefinition
Other representations of profile: CSV, Excel, Schematron
This section provides supplemental guidance for implementing the Sequence profile.