molecular-sequence-5-prime
type: StructureDefinition
node role: treeRoot
id:
  v: molecular-sequence-5-prime
text:
  status:
    v: extensions
  div: Generated Narrative: StructureDefinition molecular-sequence-5-prime Nom Drapeaux Card. Type Description et contraintes<img src="[binary]" alt="doco" style="background-color: inherit"/> MolecularSequence MolecularSequence type 0..1 code aa | dna | rna Binding: Genome entity type Value Set (required) coordinateSystem 1..1 integer Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end) Required Pattern: 0 patient 0..1 Reference(Oncology Patient) Who and/or what this is about referenceSeq 1..1 BackboneElement A sequence used as reference chromosome 0..1 CodeableConcept Fusion chromosome 5 prime Binding: GeneticMaterial (extensible) strand 0..1 code watson | crick Required Pattern: crick windowStart 0..1 integer Fusion 5 prime position <img src="[binary]" alt="doco" style="background-color: inherit"/> Documentation for this format
url:
  v: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/molecular-sequence-5-prime
version:
  v: 1.1.0
name:
  v: MolecularSequence5Prime
title:
  v: 5 Prime Molecular Sequence
status:
  v: draft
date:
  v: 2025-04-03T14:14:07+02:00
publisher:
  v: institutcancer
contact:
  name:
    v: institutcancer
  telecom:
    system:
      v: url
    value:
      v: http://cancer.fr
  telecom:
    system:
      v: email
contact:
  name:
    v: Aurélien JOBARD
  telecom:
    system:
      v: email
description:
  v: 5 prime molecular sequence is for referencing the 5' edge of a Fusion Observation.
fhir version:
  v: 4.0.1
mapping:
  identity:
    v: w5
  uri:
    v: http://hl7.org/fhir/fivews
  name:
    v: FiveWs Pattern Mapping
mapping:
  identity:
    v: rim
  uri:
    v: http://hl7.org/v3
  name:
    v: RIM Mapping
kind:
  v: resource
abstract:
  v: false
type:
  v: MolecularSequence
base definition:
  v: http://hl7.org/fhir/StructureDefinition/MolecularSequence
  link: http://hl7.org/fhir/StructureDefinition/MolecularSequence
derivation:
  v: constraint
snapshot:
  extension:
    url:
      v: http://hl7.org/fhir/tools/StructureDefinition/snapshot-base-version
    value: string
      v: 4.0.1
  element:
    id:
      v: MolecularSequence
    path:
      v: MolecularSequence
    short:
      v: Information about a biological sequence
    definition:
      v: Raw data describing a biological sequence.
    min:
      v: 0
    max:
      v: *
    base:
      path:
        v: MolecularSequence
      min:
        v: 0
      max:
        v: *
    constraint:
      key:
        v: dom-2
      severity:
        v: error
      human:
        v: If the resource is contained in another resource, it SHALL NOT contain nested Resources
      expression:
        v: contained.contained.empty()
      xpath:
        v: not(parent::f:contained and f:contained)
      source:
        v: http://hl7.org/fhir/StructureDefinition/DomainResource
        link: http://hl7.org/fhir/StructureDefinition/DomainResource
    constraint:
      key:
        v: dom-3
      severity:
        v: error
      human:
        v: 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
      expression:
        v: contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
      xpath:
        v: not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))
      source:
        v: http://hl7.org/fhir/StructureDefinition/DomainResource
        link: http://hl7.org/fhir/StructureDefinition/DomainResource
    constraint:
      key:
        v: dom-4
      severity:
        v: error
      human:
        v: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
      expression:
        v: contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
      xpath:
        v: not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))
      source:
        v: http://hl7.org/fhir/StructureDefinition/DomainResource
        link: http://hl7.org/fhir/StructureDefinition/DomainResource
    constraint:
      key:
        v: dom-5
      severity:
        v: error
      human:
        v: If a resource is contained in another resource, it SHALL NOT have a security label
      expression:
        v: contained.meta.security.empty()
      xpath:
        v: not(exists(f:contained/*/f:meta/f:security))
      source:
        v: http://hl7.org/fhir/StructureDefinition/DomainResource
        link: http://hl7.org/fhir/StructureDefinition/DomainResource
    constraint:
      extension:
        value: boolean
      extension:
        value: markdown
      key:
        v: dom-6
      severity:
        v: warning
      human:
        v: A resource should have narrative for robust management
      expression:
        v: text.`div`.exists()
      xpath:
        v: exists(f:text/h:div)
      source:
        v: http://hl7.org/fhir/StructureDefinition/DomainResource
        link: http://hl7.org/fhir/StructureDefinition/DomainResource
    constraint:
      key:
        v: msq-3
      severity:
        v: error
      human:
        v: Only 0 and 1 are valid for coordinateSystem
      expression:
        v: coordinateSystem = 1 or coordinateSystem = 0
      xpath:
        v: count(f:coordinateSystem[@value=0 and @value=1]) = 1
      source:
        v: http://hl7.org/fhir/StructureDefinition/MolecularSequence
        link: http://hl7.org/fhir/StructureDefinition/MolecularSequence
    is modifier:
      v: false
    is summary:
      v: false
    mapping:
      identity:
        v: rim
      map:
        v: Entity. Role, or Act
  element:
    id:
      v: MolecularSequence.id
    path:
      v: MolecularSequence.id
    short:
      v: Logical id of this artifact
    definition:
      v: The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
    comment:
      v: The only time that a resource does not have an id is when it is being submitted to the server using a create operation.

boolean
v: true

markdown
v: When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time.

v: 0

v: 1

path:
  v: Resource.id
min:
  v: 0
max:
  v: 1

extension:
  url:
    v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
  value: url
    v: id
code:
  v: http://hl7.org/fhirpath/System.String

v: false

v: true

id:
  v: MolecularSequence.meta
path:
  v: MolecularSequence.meta
short:
  v: Metadata about the resource
definition:
  v: The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Resource.meta
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: Meta
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.implicitRules
path:
  v: MolecularSequence.implicitRules
short:
  v: A set of rules under which this content was created
definition:
  v: A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.
comment:
  v: Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Resource.implicitRules
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: uri
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: true
is modifier reason:
  v: This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation
is summary:
  v: true

id:
  v: MolecularSequence.language
path:
  v: MolecularSequence.language
short:
  v: Language of the resource content
definition:
  v: The base language in which the resource is written.
comment:
  v: Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Resource.language
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: code
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: false
binding:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet
    value: canonical
      v: http://hl7.org/fhir/ValueSet/all-languages
      link: http://hl7.org/fhir/ValueSet/all-languages
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName
    value: string
      v: Language
  strength:
    v: preferred
  description:
    v: A human language.
  value set:
    v: http://hl7.org/fhir/ValueSet/languages
    link: http://hl7.org/fhir/ValueSet/languages

id:
  v: MolecularSequence.text
path:
  v: MolecularSequence.text
short:
  v: Text summary of the resource, for human interpretation
definition:
  v: A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.
comment:
  v: Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later.
alias:
  v: narrative
alias:
  v: html
alias:
  v: xhtml
alias:
  v: display
min:
  v: 0
max:
  v: 1
base:
  path:
    v: DomainResource.text
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: Narrative
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: Act.text?

id:
  v: MolecularSequence.contained
path:
  v: MolecularSequence.contained
short:
  v: Contained, inline Resources
definition:
  v: These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.
comment:
  v: This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.
alias:
  v: inline resources
alias:
  v: anonymous resources
alias:
  v: contained resources
min:
  v: 0
max:
  v: *
base:
  path:
    v: DomainResource.contained
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Resource
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: MolecularSequence.extension
path:
  v: MolecularSequence.extension
short:
  v: Additional content defined by implementations
definition:
  v: May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: DomainResource.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: MolecularSequence.modifierExtension
path:
  v: MolecularSequence.modifierExtension
short:
  v: Extensions that cannot be ignored
definition:
  v: May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
requirements:
  v: Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: DomainResource.modifierExtension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: true
is modifier reason:
  v: Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: MolecularSequence.identifier
path:
  v: MolecularSequence.identifier
short:
  v: Unique ID for this particular sequence. This is a FHIR-defined id
definition:
  v: A unique identifier for this particular sequence instance. This is a FHIR-defined id.
requirements:
  v: Allows sequences to be distinguished and referenced.
min:
  v: 0
max:
  v: *
base:
  path:
    v: MolecularSequence.identifier
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Identifier
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true
mapping:
  identity:
    v: w5
  map:
    v: FiveWs.identifier

id:
  v: MolecularSequence.type
path:
  v: MolecularSequence.type
short:
  v: aa | dna | rna
definition:
  v: Amino Acid Sequence/ DNA Sequence / RNA Sequence.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.type
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: code
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true
binding:
  strength:
    v: required
  value set:
    v: https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GenomeEntityType
    link: https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GenomeEntityType

id:
  v: MolecularSequence.coordinateSystem
path:
  v: MolecularSequence.coordinateSystem
short:
  v: Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
definition:
  v: Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).
min:
  v: 1
max:
  v: 1
base:
  path:
    v: MolecularSequence.coordinateSystem
  min:
    v: 1
  max:
    v: 1
type:
  code:
    v: integer
pattern: integer
  v: 0
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.patient
path:
  v: MolecularSequence.patient
short:
  v: Who and/or what this is about
definition:
  v: The patient whose sequencing results are described by this resource.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.patient
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: Reference
  target profile:
    v: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/onco-patient
    link: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/onco-patient
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.specimen
path:
  v: MolecularSequence.specimen
short:
  v: Specimen used for sequencing
definition:
  v: Specimen used for sequencing.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.specimen
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: Reference
  target profile:
    v: http://hl7.org/fhir/StructureDefinition/Specimen
    link: http://hl7.org/fhir/StructureDefinition/Specimen
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.device
path:
  v: MolecularSequence.device
short:
  v: The method for sequencing
definition:
  v: The method for sequencing, for example, chip information.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.device
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: Reference
  target profile:
    v: http://hl7.org/fhir/StructureDefinition/Device
    link: http://hl7.org/fhir/StructureDefinition/Device
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.performer
path:
  v: MolecularSequence.performer
short:
  v: Who should be responsible for test result
definition:
  v: The organization or lab that should be responsible for this result.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.performer
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: Reference
  target profile:
    v: http://hl7.org/fhir/StructureDefinition/Organization
    link: http://hl7.org/fhir/StructureDefinition/Organization
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quantity
path:
  v: MolecularSequence.quantity
short:
  v: The number of copies of the sequence of interest. (RNASeq)
definition:
  v: The number of copies of the sequence of interest. (RNASeq).
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quantity
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: Quantity
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.referenceSeq
path:
  v: MolecularSequence.referenceSeq
short:
  v: A sequence used as reference
definition:
  v: A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
min:
  v: 1
max:
  v: 1
base:
  path:
    v: MolecularSequence.referenceSeq
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: BackboneElement
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: msq-5
  severity:
    v: error
  human:
    v: GenomeBuild and chromosome must be both contained if either one of them is contained
  expression:
    v: (chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())
  xpath:
    v: (exists(f:chromosome) and exists(f:genomeBuild)) or (not(exists(f:chromosome)) and not(exists(f:genomeBuild)))
  source:
    v: http://hl7.org/fhir/StructureDefinition/MolecularSequence
    link: http://hl7.org/fhir/StructureDefinition/MolecularSequence
constraint:
  key:
    v: msq-6
  severity:
    v: error
  human:
    v: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;
  expression:
    v: (genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1
  xpath:
    v: count(f:genomeBuild)+count(f:referenceSeqId)+count(f:referenceSeqPointer)+count(f:referenceSeqString)=1
  source:
    v: http://hl7.org/fhir/StructureDefinition/MolecularSequence
    link: http://hl7.org/fhir/StructureDefinition/MolecularSequence
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.referenceSeq.id
path:
  v: MolecularSequence.referenceSeq.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: string
  code:
    v: http://hl7.org/fhirpath/System.String
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.referenceSeq.extension
path:
  v: MolecularSequence.referenceSeq.extension
short:
  v: Additional content defined by implementations
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.referenceSeq.modifierExtension
path:
  v: MolecularSequence.referenceSeq.modifierExtension
short:
  v: Extensions that cannot be ignored even if unrecognized
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
requirements:
  v: Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).
alias:
  v: extensions
alias:
  v: user content
alias:
  v: modifiers
min:
  v: 0
max:
  v: *
base:
  path:
    v: BackboneElement.modifierExtension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: true
is modifier reason:
  v: Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
is summary:
  v: true
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: MolecularSequence.referenceSeq.chromosome
path:
  v: MolecularSequence.referenceSeq.chromosome
short:
  v: Fusion chromosome 5 prime
definition:
  v: Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.referenceSeq.chromosome
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: CodeableConcept
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true
binding:
  strength:
    v: extensible
  value set:
    v: https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GeneticMaterial
    link: https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GeneticMaterial

id:
  v: MolecularSequence.referenceSeq.genomeBuild
path:
  v: MolecularSequence.referenceSeq.genomeBuild
short:
  v: The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
definition:
  v: The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.referenceSeq.genomeBuild
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: string
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.referenceSeq.orientation
path:
  v: MolecularSequence.referenceSeq.orientation
short:
  v: sense | antisense
definition:
  v: A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.referenceSeq.orientation
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: code
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true
binding:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName
    value: string
      v: orientationType
  strength:
    v: required
  description:
    v: Type for orientation.
  value set:
    v: http://hl7.org/fhir/ValueSet/orientation-type|4.0.1
    link: 4.0
    link: .1

id:
  v: MolecularSequence.referenceSeq.referenceSeqId
path:
  v: MolecularSequence.referenceSeq.referenceSeqId
short:
  v: Reference identifier
definition:
  v: Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.referenceSeq.referenceSeqId
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: CodeableConcept
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true
binding:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName
    value: string
      v: sequenceReference
  strength:
    v: example
  description:
    v: Reference identifier.
  value set:
    v: http://hl7.org/fhir/ValueSet/sequence-referenceSeq
    link: http://hl7.org/fhir/ValueSet/sequence-referenceSeq

id:
  v: MolecularSequence.referenceSeq.referenceSeqPointer
path:
  v: MolecularSequence.referenceSeq.referenceSeqPointer
short:
  v: A pointer to another MolecularSequence entity as reference sequence
definition:
  v: A pointer to another MolecularSequence entity as reference sequence.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.referenceSeq.referenceSeqPointer
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: Reference
  target profile:
    v: http://hl7.org/fhir/StructureDefinition/MolecularSequence
    link: http://hl7.org/fhir/StructureDefinition/MolecularSequence
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.referenceSeq.referenceSeqString
path:
  v: MolecularSequence.referenceSeq.referenceSeqString
short:
  v: A string to represent reference sequence
definition:
  v: A string like "ACGT".
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.referenceSeq.referenceSeqString
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: string
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.referenceSeq.strand
path:
  v: MolecularSequence.referenceSeq.strand
short:
  v: watson | crick
definition:
  v: An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.referenceSeq.strand
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: code
pattern: code
  v: crick
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true
binding:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName
    value: string
      v: strandType
  strength:
    v: required
  description:
    v: Type for strand.
  value set:
    v: http://hl7.org/fhir/ValueSet/strand-type|4.0.1
    link: 4.0
    link: .1

id:
  v: MolecularSequence.referenceSeq.windowStart
path:
  v: MolecularSequence.referenceSeq.windowStart
short:
  v: Fusion 5 prime position
definition:
  v: Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.referenceSeq.windowStart
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.referenceSeq.windowEnd
path:
  v: MolecularSequence.referenceSeq.windowEnd
short:
  v: End position of the window on the reference sequence
definition:
  v: End position of the window on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.referenceSeq.windowEnd
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.variant
path:
  v: MolecularSequence.variant
short:
  v: Variant in sequence
definition:
  v: The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.
min:
  v: 0
max:
  v: *
base:
  path:
    v: MolecularSequence.variant
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: BackboneElement
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.variant.id
path:
  v: MolecularSequence.variant.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: string
  code:
    v: http://hl7.org/fhirpath/System.String
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.variant.extension
path:
  v: MolecularSequence.variant.extension
short:
  v: Additional content defined by implementations
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.variant.modifierExtension
path:
  v: MolecularSequence.variant.modifierExtension
short:
  v: Extensions that cannot be ignored even if unrecognized
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
requirements:
  v: Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).
alias:
  v: extensions
alias:
  v: user content
alias:
  v: modifiers
min:
  v: 0
max:
  v: *
base:
  path:
    v: BackboneElement.modifierExtension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: true
is modifier reason:
  v: Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
is summary:
  v: true
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: MolecularSequence.variant.start
path:
  v: MolecularSequence.variant.start
short:
  v: Start position of the variant on the reference sequence
definition:
  v: Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.variant.start
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.variant.end
path:
  v: MolecularSequence.variant.end
short:
  v: End position of the variant on the reference sequence
definition:
  v: End position of the variant on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.variant.end
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.variant.observedAllele
path:
  v: MolecularSequence.variant.observedAllele
short:
  v: Allele that was observed
definition:
  v: An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.variant.observedAllele
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: string
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.variant.referenceAllele
path:
  v: MolecularSequence.variant.referenceAllele
short:
  v: Allele in the reference sequence
definition:
  v: An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.variant.referenceAllele
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: string
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.variant.cigar
path:
  v: MolecularSequence.variant.cigar
short:
  v: Extended CIGAR string for aligning the sequence with reference bases
definition:
  v: Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.variant.cigar
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: string
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.variant.variantPointer
path:
  v: MolecularSequence.variant.variantPointer
short:
  v: Pointer to observed variant information
definition:
  v: A pointer to an Observation containing variant information.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.variant.variantPointer
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: Reference
  target profile:
    v: http://hl7.org/fhir/StructureDefinition/Observation
    link: http://hl7.org/fhir/StructureDefinition/Observation
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.observedSeq
path:
  v: MolecularSequence.observedSeq
short:
  v: Sequence that was observed
definition:
  v: Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.observedSeq
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: string
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality
path:
  v: MolecularSequence.quality
short:
  v: An set of value as quality of sequence
definition:
  v: An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).
min:
  v: 0
max:
  v: *
base:
  path:
    v: MolecularSequence.quality
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: BackboneElement
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.id
path:
  v: MolecularSequence.quality.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: string
  code:
    v: http://hl7.org/fhirpath/System.String
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.quality.extension
path:
  v: MolecularSequence.quality.extension
short:
  v: Additional content defined by implementations
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.quality.modifierExtension
path:
  v: MolecularSequence.quality.modifierExtension
short:
  v: Extensions that cannot be ignored even if unrecognized
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
requirements:
  v: Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).
alias:
  v: extensions
alias:
  v: user content
alias:
  v: modifiers
min:
  v: 0
max:
  v: *
base:
  path:
    v: BackboneElement.modifierExtension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: true
is modifier reason:
  v: Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
is summary:
  v: true
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: MolecularSequence.quality.type
path:
  v: MolecularSequence.quality.type
short:
  v: indel | snp | unknown
definition:
  v: INDEL / SNP / Undefined variant.
min:
  v: 1
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.type
  min:
    v: 1
  max:
    v: 1
type:
  code:
    v: code
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true
binding:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName
    value: string
      v: qualityType
  strength:
    v: required
  description:
    v: Type for quality report.
  value set:
    v: http://hl7.org/fhir/ValueSet/quality-type|4.0.1
    link: 4.0
    link: .1

id:
  v: MolecularSequence.quality.standardSequence
path:
  v: MolecularSequence.quality.standardSequence
short:
  v: Standard sequence for comparison
definition:
  v: Gold standard sequence used for comparing against.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.standardSequence
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: CodeableConcept
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true
binding:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName
    value: string
      v: qualityStandardSequence
  strength:
    v: example
  description:
    v: Reference identifier of the sequence that used to mark the quality of tested samples.
  value set:
    v: http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence
    link: http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence

id:
  v: MolecularSequence.quality.start
path:
  v: MolecularSequence.quality.start
short:
  v: Start position of the sequence
definition:
  v: Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.start
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.end
path:
  v: MolecularSequence.quality.end
short:
  v: End position of the sequence
definition:
  v: End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.end
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.score
path:
  v: MolecularSequence.quality.score
short:
  v: Quality score for the comparison
definition:
  v: The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.score
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: Quantity
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.method
path:
  v: MolecularSequence.quality.method
short:
  v: Method to get quality
definition:
  v: Which method is used to get sequence quality.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.method
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: CodeableConcept
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true
binding:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName
    value: string
      v: qualityMethod
  strength:
    v: example
  description:
    v: The method used to evaluate the numerical quality of the observed sequence.
  value set:
    v: http://hl7.org/fhir/ValueSet/sequence-quality-method
    link: http://hl7.org/fhir/ValueSet/sequence-quality-method

id:
  v: MolecularSequence.quality.truthTP
path:
  v: MolecularSequence.quality.truthTP
short:
  v: True positives from the perspective of the truth data
definition:
  v: True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.truthTP
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.queryTP
path:
  v: MolecularSequence.quality.queryTP
short:
  v: True positives from the perspective of the query data
definition:
  v: True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.queryTP
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.truthFN
path:
  v: MolecularSequence.quality.truthFN
short:
  v: False negatives
definition:
  v: False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.truthFN
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.queryFP
path:
  v: MolecularSequence.quality.queryFP
short:
  v: False positives
definition:
  v: False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.queryFP
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.gtFP
path:
  v: MolecularSequence.quality.gtFP
short:
  v: False positives where the non-REF alleles in the Truth and Query Call Sets match
definition:
  v: The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.gtFP
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.precision
path:
  v: MolecularSequence.quality.precision
short:
  v: Precision of comparison
definition:
  v: QUERY.TP / (QUERY.TP + QUERY.FP).
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.precision
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.recall
path:
  v: MolecularSequence.quality.recall
short:
  v: Recall of comparison
definition:
  v: TRUTH.TP / (TRUTH.TP + TRUTH.FN).
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.recall
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.fScore
path:
  v: MolecularSequence.quality.fScore
short:
  v: F-score
definition:
  v: Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.fScore
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: decimal
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.roc
path:
  v: MolecularSequence.quality.roc
short:
  v: Receiver Operator Characteristic (ROC) Curve
definition:
  v: Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.quality.roc
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: BackboneElement
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.roc.id
path:
  v: MolecularSequence.quality.roc.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: string
  code:
    v: http://hl7.org/fhirpath/System.String
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.quality.roc.extension
path:
  v: MolecularSequence.quality.roc.extension
short:
  v: Additional content defined by implementations
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.quality.roc.modifierExtension
path:
  v: MolecularSequence.quality.roc.modifierExtension
short:
  v: Extensions that cannot be ignored even if unrecognized
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
requirements:
  v: Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).
alias:
  v: extensions
alias:
  v: user content
alias:
  v: modifiers
min:
  v: 0
max:
  v: *
base:
  path:
    v: BackboneElement.modifierExtension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: true
is modifier reason:
  v: Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
is summary:
  v: true
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: MolecularSequence.quality.roc.score
path:
  v: MolecularSequence.quality.roc.score
short:
  v: Genotype quality score
definition:
  v: Invidual data point representing the GQ (genotype quality) score threshold.
min:
  v: 0
max:
  v: *
base:
  path:
    v: MolecularSequence.quality.roc.score
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.roc.numTP
path:
  v: MolecularSequence.quality.roc.numTP
short:
  v: Roc score true positive numbers
definition:
  v: The number of true positives if the GQ score threshold was set to "score" field value.
min:
  v: 0
max:
  v: *
base:
  path:
    v: MolecularSequence.quality.roc.numTP
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.roc.numFP
path:
  v: MolecularSequence.quality.roc.numFP
short:
  v: Roc score false positive numbers
definition:
  v: The number of false positives if the GQ score threshold was set to "score" field value.
min:
  v: 0
max:
  v: *
base:
  path:
    v: MolecularSequence.quality.roc.numFP
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.roc.numFN
path:
  v: MolecularSequence.quality.roc.numFN
short:
  v: Roc score false negative numbers
definition:
  v: The number of false negatives if the GQ score threshold was set to "score" field value.
min:
  v: 0
max:
  v: *
base:
  path:
    v: MolecularSequence.quality.roc.numFN
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.roc.precision
path:
  v: MolecularSequence.quality.roc.precision
short:
  v: Precision of the GQ score
definition:
  v: Calculated precision if the GQ score threshold was set to "score" field value.
min:
  v: 0
max:
  v: *
base:
  path:
    v: MolecularSequence.quality.roc.precision
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: decimal
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.roc.sensitivity
path:
  v: MolecularSequence.quality.roc.sensitivity
short:
  v: Sensitivity of the GQ score
definition:
  v: Calculated sensitivity if the GQ score threshold was set to "score" field value.
min:
  v: 0
max:
  v: *
base:
  path:
    v: MolecularSequence.quality.roc.sensitivity
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: decimal
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.quality.roc.fMeasure
path:
  v: MolecularSequence.quality.roc.fMeasure
short:
  v: FScore of the GQ score
definition:
  v: Calculated fScore if the GQ score threshold was set to "score" field value.
min:
  v: 0
max:
  v: *
base:
  path:
    v: MolecularSequence.quality.roc.fMeasure
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: decimal
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.readCoverage
path:
  v: MolecularSequence.readCoverage
short:
  v: Average number of reads representing a given nucleotide in the reconstructed sequence
definition:
  v: Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.readCoverage
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.repository
path:
  v: MolecularSequence.repository
short:
  v: External repository which contains detailed report related with observedSeq in this resource
definition:
  v: Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
min:
  v: 0
max:
  v: *
base:
  path:
    v: MolecularSequence.repository
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: BackboneElement
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.repository.id
path:
  v: MolecularSequence.repository.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: string
  code:
    v: http://hl7.org/fhirpath/System.String
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.repository.extension
path:
  v: MolecularSequence.repository.extension
short:
  v: Additional content defined by implementations
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.repository.modifierExtension
path:
  v: MolecularSequence.repository.modifierExtension
short:
  v: Extensions that cannot be ignored even if unrecognized
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
requirements:
  v: Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).
alias:
  v: extensions
alias:
  v: user content
alias:
  v: modifiers
min:
  v: 0
max:
  v: *
base:
  path:
    v: BackboneElement.modifierExtension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: true
is modifier reason:
  v: Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
is summary:
  v: true
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: MolecularSequence.repository.type
path:
  v: MolecularSequence.repository.type
short:
  v: directlink | openapi | login | oauth | other
definition:
  v: Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.
min:
  v: 1
max:
  v: 1
base:
  path:
    v: MolecularSequence.repository.type
  min:
    v: 1
  max:
    v: 1
type:
  code:
    v: code
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true
binding:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName
    value: string
      v: repositoryType
  strength:
    v: required
  description:
    v: Type for access of external URI.
  value set:
    v: http://hl7.org/fhir/ValueSet/repository-type|4.0.1
    link: 4.0
    link: .1

id:
  v: MolecularSequence.repository.url
path:
  v: MolecularSequence.repository.url
short:
  v: URI of the repository
definition:
  v: URI of an external repository which contains further details about the genetics data.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.repository.url
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: uri
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.repository.name
path:
  v: MolecularSequence.repository.name
short:
  v: Repository's name
definition:
  v: URI of an external repository which contains further details about the genetics data.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.repository.name
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: string
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.repository.datasetId
path:
  v: MolecularSequence.repository.datasetId
short:
  v: Id of the dataset that used to call for dataset in repository
definition:
  v: Id of the variant in this external repository. The server will understand how to use this id to call for more info about datasets in external repository.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.repository.datasetId
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: string
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.repository.variantsetId
path:
  v: MolecularSequence.repository.variantsetId
short:
  v: Id of the variantset that used to call for variantset in repository
definition:
  v: Id of the variantset in this external repository. The server will understand how to use this id to call for more info about variantsets in external repository.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.repository.variantsetId
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: string
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.repository.readsetId
path:
  v: MolecularSequence.repository.readsetId
short:
  v: Id of the read
definition:
  v: Id of the read in this external repository.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.repository.readsetId
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: string
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.pointer
path:
  v: MolecularSequence.pointer
short:
  v: Pointer to next atomic sequence
definition:
  v: Pointer to next atomic sequence which at most contains one variant.
min:
  v: 0
max:
  v: *
base:
  path:
    v: MolecularSequence.pointer
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Reference
  target profile:
    v: http://hl7.org/fhir/StructureDefinition/MolecularSequence
    link: http://hl7.org/fhir/StructureDefinition/MolecularSequence
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.structureVariant
path:
  v: MolecularSequence.structureVariant
short:
  v: Structural variant
definition:
  v: Information about chromosome structure variation.
min:
  v: 0
max:
  v: *
base:
  path:
    v: MolecularSequence.structureVariant
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: BackboneElement
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.structureVariant.id
path:
  v: MolecularSequence.structureVariant.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: string
  code:
    v: http://hl7.org/fhirpath/System.String
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.structureVariant.extension
path:
  v: MolecularSequence.structureVariant.extension
short:
  v: Additional content defined by implementations
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.structureVariant.modifierExtension
path:
  v: MolecularSequence.structureVariant.modifierExtension
short:
  v: Extensions that cannot be ignored even if unrecognized
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
requirements:
  v: Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).
alias:
  v: extensions
alias:
  v: user content
alias:
  v: modifiers
min:
  v: 0
max:
  v: *
base:
  path:
    v: BackboneElement.modifierExtension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: true
is modifier reason:
  v: Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
is summary:
  v: true
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: MolecularSequence.structureVariant.variantType
path:
  v: MolecularSequence.structureVariant.variantType
short:
  v: Structural variant change type
definition:
  v: Information about chromosome structure variation DNA change type.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.structureVariant.variantType
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: CodeableConcept
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true
binding:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName
    value: string
      v: LOINC LL379-9 answerlist
  strength:
    v: required
  description:
    v: DNA change type.
  value set:
    v: http://loinc.org/vs/LL379-9|4.0.1
    link: 4.0
    link: .1

id:
  v: MolecularSequence.structureVariant.exact
path:
  v: MolecularSequence.structureVariant.exact
short:
  v: Does the structural variant have base pair resolution breakpoints?
definition:
  v: Used to indicate if the outer and inner start-end values have the same meaning.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.structureVariant.exact
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: boolean
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.structureVariant.length
path:
  v: MolecularSequence.structureVariant.length
short:
  v: Structural variant length
definition:
  v: Length of the variant chromosome.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.structureVariant.length
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.structureVariant.outer
path:
  v: MolecularSequence.structureVariant.outer
short:
  v: Structural variant outer
definition:
  v: Structural variant outer.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.structureVariant.outer
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: BackboneElement
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.structureVariant.outer.id
path:
  v: MolecularSequence.structureVariant.outer.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: string
  code:
    v: http://hl7.org/fhirpath/System.String
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.structureVariant.outer.extension
path:
  v: MolecularSequence.structureVariant.outer.extension
short:
  v: Additional content defined by implementations
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.structureVariant.outer.modifierExtension
path:
  v: MolecularSequence.structureVariant.outer.modifierExtension
short:
  v: Extensions that cannot be ignored even if unrecognized
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
requirements:
  v: Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).
alias:
  v: extensions
alias:
  v: user content
alias:
  v: modifiers
min:
  v: 0
max:
  v: *
base:
  path:
    v: BackboneElement.modifierExtension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: true
is modifier reason:
  v: Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
is summary:
  v: true
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: MolecularSequence.structureVariant.outer.start
path:
  v: MolecularSequence.structureVariant.outer.start
short:
  v: Structural variant outer start
definition:
  v: Structural variant outer start. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.structureVariant.outer.start
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.structureVariant.outer.end
path:
  v: MolecularSequence.structureVariant.outer.end
short:
  v: Structural variant outer end
definition:
  v: Structural variant outer end. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.structureVariant.outer.end
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.structureVariant.inner
path:
  v: MolecularSequence.structureVariant.inner
short:
  v: Structural variant inner
definition:
  v: Structural variant inner.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.structureVariant.inner
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: BackboneElement
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.structureVariant.inner.id
path:
  v: MolecularSequence.structureVariant.inner.id
representation:
  v: xmlAttr
short:
  v: Unique id for inter-element referencing
definition:
  v: Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: Element.id
  min:
    v: 0
  max:
    v: 1
type:
  extension:
    url:
      v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type
    value: url
      v: string
  code:
    v: http://hl7.org/fhirpath/System.String
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.structureVariant.inner.extension
path:
  v: MolecularSequence.structureVariant.inner.extension
short:
  v: Additional content defined by implementations
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
alias:
  v: extensions
alias:
  v: user content
min:
  v: 0
max:
  v: *
base:
  path:
    v: Element.extension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: false
is summary:
  v: false
mapping:
  identity:
    v: rim
  map:
    v: n/a

id:
  v: MolecularSequence.structureVariant.inner.modifierExtension
path:
  v: MolecularSequence.structureVariant.inner.modifierExtension
short:
  v: Extensions that cannot be ignored even if unrecognized
definition:
  v: May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).
comment:
  v: There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
requirements:
  v: Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).
alias:
  v: extensions
alias:
  v: user content
alias:
  v: modifiers
min:
  v: 0
max:
  v: *
base:
  path:
    v: BackboneElement.modifierExtension
  min:
    v: 0
  max:
    v: *
type:
  code:
    v: Extension
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
constraint:
  key:
    v: ext-1
  severity:
    v: error
  human:
    v: Must have either extensions or value[x], not both
  expression:
    v: extension.exists() != value.exists()
  xpath:
    v: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
  source:
    v: http://hl7.org/fhir/StructureDefinition/Extension
    link: http://hl7.org/fhir/StructureDefinition/Extension
is modifier:
  v: true
is modifier reason:
  v: Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
is summary:
  v: true
mapping:
  identity:
    v: rim
  map:
    v: N/A

id:
  v: MolecularSequence.structureVariant.inner.start
path:
  v: MolecularSequence.structureVariant.inner.start
short:
  v: Structural variant inner start
definition:
  v: Structural variant inner start. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.structureVariant.inner.start
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

id:
  v: MolecularSequence.structureVariant.inner.end
path:
  v: MolecularSequence.structureVariant.inner.end
short:
  v: Structural variant inner end
definition:
  v: Structural variant inner end. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
min:
  v: 0
max:
  v: 1
base:
  path:
    v: MolecularSequence.structureVariant.inner.end
  min:
    v: 0
  max:
    v: 1
type:
  code:
    v: integer
constraint:
  key:
    v: ele-1
  severity:
    v: error
  human:
    v: All FHIR elements must have a @value or children
  expression:
    v: hasValue() or (children().count() > id.count())
  xpath:
    v: @value|f:*|h:div
  source:
    v: http://hl7.org/fhir/StructureDefinition/Element
    link: http://hl7.org/fhir/StructureDefinition/Element
is modifier:
  v: false
is summary:
  v: true

element:
  id:
    v: MolecularSequence.type
  path:
    v: MolecularSequence.type
  binding:
    strength:
      v: required
    value set:
      v: https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GenomeEntityType
      link: https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GenomeEntityType
element:
  id:
    v: MolecularSequence.coordinateSystem
  path:
    v: MolecularSequence.coordinateSystem
  pattern: integer
    v: 0
element:
  id:
    v: MolecularSequence.patient
  path:
    v: MolecularSequence.patient
  type:
    code:
      v: Reference
    target profile:
      v: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/onco-patient
      link: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/onco-patient
element:
  id:
    v: MolecularSequence.referenceSeq
  path:
    v: MolecularSequence.referenceSeq
  min:
    v: 1
element:
  id:
    v: MolecularSequence.referenceSeq.chromosome
  path:
    v: MolecularSequence.referenceSeq.chromosome
  short:
    v: Fusion chromosome 5 prime
  binding:
    strength:
      v: extensible
    value set:
      v: https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GeneticMaterial
      link: https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GeneticMaterial
element:
  id:
    v: MolecularSequence.referenceSeq.strand
  path:
    v: MolecularSequence.referenceSeq.strand
  pattern: code
    v: crick
element:
  id:
    v: MolecularSequence.referenceSeq.windowStart
  path:
    v: MolecularSequence.referenceSeq.windowStart
  short:
    v: Fusion 5 prime position