Molecular Definition Implementation Guide for Molecular Data Types
1.0.0-ballot1 - ci-build International flag

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

Resource Profile: Haplotype ( Experimental )

Official URL: http://hl7.org/fhir/uv/molecular-definition-data-types/StructureDefinition/haplotype Version: 1.0.0-ballot1
Standards status: Informative Computable Name: Haplotype

Haplotype profile of MolecularDefinition Resource

Scope and Usage

The Haplotype profile is designed to represent genomic haplotypes as collections of alleles that reside in a cis configuration. It utilizes the member element to reference one or more alleles, each defined through the Allele profile. The location element is not used directly in the Haplotype profile; instead, genomic locations are conveyed through the referenced member alleles. This structure enables precise representation of complex genetic makeup in a unified way.

Usages:

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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
... topology Σ 0..* CodeableConcept The structural topology of the molecular entity (e.g., linear, circular)
Binding: Topology ValueSet (required)
... member SΣ 0..* Reference(Allele) Constituents of an aggregate molecular concept (e.g., haplotype, genotype)

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
MolecularDefinition.​type Base required Molecule Type ValueSet 📦1.0.0-ballot1 This IG
MolecularDefinition.​topology Base required Topology ValueSet 📦1.0.0-ballot1 This IG

Constraints

Id Grade Path(s) Description Expression
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

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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) Constituents of an aggregate molecular concept (e.g., haplotype, genotype)
... representation
.... literal 0..0
.... extracted 0..0
.... repeated 0..0
.... concatenated 0..0
.... relative 0..0

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
MolecularDefinition.​type Base required Molecule Type ValueSet 📦1.0.0-ballot1 This IG
MolecularDefinition.​topology Base required Topology ValueSet 📦1.0.0-ballot1 This IG
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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
... 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) 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
.... resolvable Σ 0..1 Reference(DocumentReference) A resolvable representation of a molecular entity (e.g., URI, attached and formatted file)

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
MolecularDefinition.​language Base required All Languages 📍6.0.0-ballot3 FHIR Std.
MolecularDefinition.​type Base required Molecule Type ValueSet 📦1.0.0-ballot1 This IG
MolecularDefinition.​topology Base required Topology ValueSet 📦1.0.0-ballot1 This IG
MolecularDefinition.​location.sequenceLocation.​coordinateInterval.coordinateSystem.​system Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
MolecularDefinition.​representation.extracted.​coordinateInterval.coordinateSystem.​system Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
MolecularDefinition.​representation.relative.​edit.coordinateInterval.​coordinateSystem.system Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?

Constraints

Id Grade Path(s) Description Expression
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

Summary

Mandatory: 1 element
Must-Support: 2 elements
Prohibited: 6 elements

Structures

This structure refers to these other structures:

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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
... topology Σ 0..* CodeableConcept The structural topology of the molecular entity (e.g., linear, circular)
Binding: Topology ValueSet (required)
... member SΣ 0..* Reference(Allele) Constituents of an aggregate molecular concept (e.g., haplotype, genotype)

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
MolecularDefinition.​type Base required Molecule Type ValueSet 📦1.0.0-ballot1 This IG
MolecularDefinition.​topology Base required Topology ValueSet 📦1.0.0-ballot1 This IG

Constraints

Id Grade Path(s) Description Expression
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

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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) Constituents of an aggregate molecular concept (e.g., haplotype, genotype)
... representation
.... literal 0..0
.... extracted 0..0
.... repeated 0..0
.... concatenated 0..0
.... relative 0..0

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
MolecularDefinition.​type Base required Molecule Type ValueSet 📦1.0.0-ballot1 This IG
MolecularDefinition.​topology Base required Topology ValueSet 📦1.0.0-ballot1 This IG

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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
... 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) 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
.... resolvable Σ 0..1 Reference(DocumentReference) A resolvable representation of a molecular entity (e.g., URI, attached and formatted file)

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
MolecularDefinition.​language Base required All Languages 📍6.0.0-ballot3 FHIR Std.
MolecularDefinition.​type Base required Molecule Type ValueSet 📦1.0.0-ballot1 This IG
MolecularDefinition.​topology Base required Topology ValueSet 📦1.0.0-ballot1 This IG
MolecularDefinition.​location.sequenceLocation.​coordinateInterval.coordinateSystem.​system Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
MolecularDefinition.​representation.extracted.​coordinateInterval.coordinateSystem.​system Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
MolecularDefinition.​representation.relative.​edit.coordinateInterval.​coordinateSystem.system Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?

Constraints

Id Grade Path(s) Description Expression
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

Summary

Mandatory: 1 element
Must-Support: 2 elements
Prohibited: 6 elements

Structures

This structure refers to these other structures:

 

Other representations of profile: CSV, Excel, Schematron