Molecular Definition Implementation Guide for Molecular Data Types
1.0.0-ballot1 - ci-build
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/genotype | Version: 1.0.0-ballot1 | |||
| Standards status: Informative | Computable Name: Genotype | |||
Genotype profile of Molecular Definition
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:   |
|---|---|---|---|---|
  MolecularDefinition |
0..* | MolecularDefinition | Definitional content for a molecular entity | |
  implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created |
| contained |
0..* | Resource | Contained, inline Resources | |
 modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored |
 type |
SΣ | 1..1 | CodeableConcept | Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type (required) |
| topology |
Σ | 0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology (required) |
  member |
SΣ | 0..* | Reference(Allele | Haplotype) | Constituents of an aggregate molecular concept (e.g., haplotype, genotype) |
| Documentation for this format | ||||
| 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-typeFrom this IG | |
| MolecularDefinition.topology | required | TopologyVS(a valid code from Topology)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topologyFrom 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
| Name | Flags | Card. | Type | Description & Constraints Filter: |
|---|---|---|---|---|
| MolecularDefinition |
0..* | MolecularDefinition | Definitional content for a molecular entity | |
 type |
S | 1..1 | CodeableConcept | Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type (required) |
| topology |
0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology (required) | |
| member |
S | 0..* | Reference(Allele | Haplotype) | Constituents of an aggregate molecular concept (e.g., haplotype, genotype) |
| location |
0..0 | |||
 representation |
||||
 extracted |
0..0 | |||
| repeated |
0..0 | |||
| concatenated |
0..0 | |||
| relative |
0..0 | |||
| Documentation for this format | ||||
| 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-typeFrom this IG | |
| MolecularDefinition.topology | required | TopologyVS(a valid code from Topology)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topologyFrom this IG |
| Name | Flags | Card. | Type | Description & Constraints Filter: | ||||
|---|---|---|---|---|---|---|---|---|
| MolecularDefinition |
0..* | MolecularDefinition | Definitional content for a molecular entity | |||||
| id |
Σ | 0..1 | id | Logical id of this artifact | ||||
| meta |
Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language |
0..1 | code | Language of the resource content Binding: AllLanguages (required): IETF language tag for a human language
| |||||
| text |
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 | |||||
| contained |
0..* | Resource | Contained, inline Resources | |||||
 extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
Σ | 0..* | Identifier | Unique ID of an instance | ||||
| description |
0..1 | markdown | Description of the Molecular Definition instance | |||||
| moleculeType |
Σ | 0..1 | CodeableConcept | The type of molecule (e.g., DNA, RNA, amino acid) | ||||
| type |
SΣ | 1..1 | CodeableConcept | Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type (required) | ||||
| topology |
Σ | 0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology (required) | ||||
| member |
SΣ | 0..* | Reference(Allele | Haplotype) | Constituents of an aggregate molecular concept (e.g., haplotype, genotype) | ||||
| representation |
Σ | 0..* | BackboneElement | A representation of a molecular entity | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| focus |
Σ | 0..1 | CodeableConcept | The domain concept that is the focus of a given instance of the representation | ||||
| code |
Σ | 0..* | CodeableConcept | A code (e.g., sequence accession number) used to represent a molecular entity | ||||
 literal |
Σ | 0..1 | BackboneElement | A molecular entity defined as a string literal | ||||
 id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| encoding |
Σ | 0..1 | CodeableConcept | The encoding used in the value | ||||
| value |
Σ | 1..1 | string | A string literal representation of the molecular entity, using the encoding specified in encoding | ||||
| resolvable |
Σ | 0..1 | Reference(DocumentReference) | A resolvable representation of a molecular entity (e.g., URI, attached and formatted file) | ||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet | URI |
| MolecularDefinition.language | required | AllLanguageshttp://hl7.org/fhir/ValueSet/all-languages|6.0.0-ballot3From the FHIR Standard | |
| MolecularDefinition.type | required | MoleculeTypeVS(a valid code from Molecule Type)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-typeFrom this IG | |
| MolecularDefinition.topology | required | TopologyVS(a valid code from Topology)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topologyFrom this IG | |
| MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.system | extensible | LOINC LL5323-2http://loinc.org/vs/LL5323-2 | |
| 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: |
|---|---|---|---|---|
| MolecularDefinition |
0..* | MolecularDefinition | Definitional content for a molecular entity | |
| implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created |
| contained |
0..* | Resource | Contained, inline Resources | |
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored |
| type |
SΣ | 1..1 | CodeableConcept | Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type (required) |
| topology |
Σ | 0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology (required) |
| member |
SΣ | 0..* | Reference(Allele | Haplotype) | Constituents of an aggregate molecular concept (e.g., haplotype, genotype) |
| Documentation for this format | ||||
| 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-typeFrom this IG | |
| MolecularDefinition.topology | required | TopologyVS(a valid code from Topology)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topologyFrom 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: |
|---|---|---|---|---|
| MolecularDefinition |
0..* | MolecularDefinition | Definitional content for a molecular entity | |
| type |
S | 1..1 | CodeableConcept | Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type (required) |
| topology |
0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology (required) | |
| member |
S | 0..* | Reference(Allele | Haplotype) | Constituents of an aggregate molecular concept (e.g., haplotype, genotype) |
| location |
0..0 | |||
| representation |
||||
| extracted |
0..0 | |||
| repeated |
0..0 | |||
| concatenated |
0..0 | |||
| relative |
0..0 | |||
| Documentation for this format | ||||
| 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-typeFrom this IG | |
| MolecularDefinition.topology | required | TopologyVS(a valid code from Topology)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topologyFrom this IG |
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints Filter: | ||||
|---|---|---|---|---|---|---|---|---|
| MolecularDefinition |
0..* | MolecularDefinition | Definitional content for a molecular entity | |||||
| id |
Σ | 0..1 | id | Logical id of this artifact | ||||
| meta |
Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language |
0..1 | code | Language of the resource content Binding: AllLanguages (required): IETF language tag for a human language
| |||||
| text |
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 | |||||
| contained |
0..* | Resource | Contained, inline Resources | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
Σ | 0..* | Identifier | Unique ID of an instance | ||||
| description |
0..1 | markdown | Description of the Molecular Definition instance | |||||
| moleculeType |
Σ | 0..1 | CodeableConcept | The type of molecule (e.g., DNA, RNA, amino acid) | ||||
| type |
SΣ | 1..1 | CodeableConcept | Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type (required) | ||||
| topology |
Σ | 0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology (required) | ||||
| member |
SΣ | 0..* | Reference(Allele | Haplotype) | Constituents of an aggregate molecular concept (e.g., haplotype, genotype) | ||||
| representation |
Σ | 0..* | BackboneElement | A representation of a molecular entity | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| focus |
Σ | 0..1 | CodeableConcept | The domain concept that is the focus of a given instance of the representation | ||||
| code |
Σ | 0..* | CodeableConcept | A code (e.g., sequence accession number) used to represent a molecular entity | ||||
| literal |
Σ | 0..1 | BackboneElement | A molecular entity defined as a string literal | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| encoding |
Σ | 0..1 | CodeableConcept | The encoding used in the value | ||||
| value |
Σ | 1..1 | string | A string literal representation of the molecular entity, using the encoding specified in encoding | ||||
| resolvable |
Σ | 0..1 | Reference(DocumentReference) | A resolvable representation of a molecular entity (e.g., URI, attached and formatted file) | ||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet | URI |
| MolecularDefinition.language | required | AllLanguageshttp://hl7.org/fhir/ValueSet/all-languages|6.0.0-ballot3From the FHIR Standard | |
| MolecularDefinition.type | required | MoleculeTypeVS(a valid code from Molecule Type)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-typeFrom this IG | |
| MolecularDefinition.topology | required | TopologyVS(a valid code from Topology)http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topologyFrom this IG | |
| MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.system | extensible | LOINC LL5323-2http://loinc.org/vs/LL5323-2 | |
| 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