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 MolecularDefinition
The Genotype profile is intended to represent genomic genotypes as collections of alleles and haplotypes arranged in either cis or trans configurations.
It employs the member element to reference one or more alleles and/or haplotypes, each defined using the Allele and Haplotype profiles, respectively. As with the Haplotype profile, the location element is not used directly in the Genotype profile; genomic locations are instead conveyed through the referenced member alleles. This structure offers a comprehensive and accurate way for representing complex genetic makeup.
Usages:
You can also check for usages in the FHIR IG Statistics
Description of Profiles, Differentials, Snapshots and how the different presentations work.
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 ValueSet (required) |
| topology |
0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology ValueSet (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 | |
 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 ValueSet (required) |
| topology |
Σ | 0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology ValueSet (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()) |
| 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 ValueSet (required) | ||||
| topology |
Σ | 0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology ValueSet (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
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 ValueSet (required) |
| topology |
0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology ValueSet (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 |
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 ValueSet (required) |
| topology |
Σ | 0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology ValueSet (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()) |
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 ValueSet (required) | ||||
| topology |
Σ | 0..* | CodeableConcept | The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology ValueSet (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
IG © 2025+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.molecular-definition-data-types#1.0.0-ballot1 based on FHIR 6.0.0-ballot3. Generated 2025-09-22
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