FHIR Osiris Implementation Guide
1.1.0 - trial-implementation

Publication Build: This will be filled in by the publication tooling

## Resource Profile: AnnotationReference - Detailed Descriptions

Draft as of 2025-04-03

Definitions for the annotation-reference resource profile.

- Key Elements Table
- Differential Elements Table
- Snapshot Elements Table

Guidance on how to interpret the contents of this table can be found here

0. MolecularSequence
Définition | Raw data describing a biological sequence.
Short | Information about a biological sequence
Control | 0..*
Is Modifier | false
Résumé | false
Invariants | dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources (contained.contained.empty()) dom-3: If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource (contained.where((('#'+id 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()) dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated (contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()) dom-5: If a resource is contained in another resource, it SHALL NOT have a security label (contained.meta.security.empty()) dom-6: A resource should have narrative for robust management (text.`div`.exists()) msq-3: Only 0 and 1 are valid for coordinateSystem (`coordinateSystem = 1 or coordinateSystem = 0`) msq-3: Only 0 and 1 are valid for coordinateSystem (coordinateSystem = 1 or coordinateSystem = 0)
2. MolecularSequence.implicitRules
Définition | 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.
Short | A set of rules under which this content was created
Commentaires | 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.
Control | 0..1
Type | uri
Is Modifier | true because 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
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
4. MolecularSequence.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
Résumé | false
Requirements | 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.
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
6. MolecularSequence.coordinateSystem
Définition | 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).
Short | 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)
Control | 1..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Pattern Value | `0`
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
8. MolecularSequence.patient
Définition | The patient whose sequencing results are described by this resource.
Short | Who and/or what this is about
Control | 0..1
Type | Reference(Oncology Patient, Patient)
Is Modifier | false
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
10. MolecularSequence.referenceSeq
Définition | A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
Short | A sequence used as reference
Control | 0..1
Type | BackboneElement
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained (`(chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())`) msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString; (`(genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1`) msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained ((chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())) msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString; ((genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1)
12. MolecularSequence.referenceSeq.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
14. MolecularSequence.referenceSeq.orientation
Définition | Strand orientation of the annotation DNA 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.
Short | DNA strand orientationsense | antisense
Control | 0..1
Binding | The codes SHALL be taken from orientationType http://hl7.org/fhir/ValueSet/orientation-type|4.0.1 (required to `http://hl7.org/fhir/ValueSet/orientation-type|4.0.1` ) Type for orientation.
Type | code
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
16. MolecularSequence.referenceSeq.referenceSeqId
Définition | Type of the annotation referenced to describe the molecular entity 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.
Short | Type of the referenced annotationReference identifier
Control | 10..1
Binding | Unless not suitable, these codes SHALL be taken from For example codes, see Reference Type Value Set http://hl7.org/fhir/ValueSet/sequence-referenceSeq (extensible to `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/ReferenceType` )
Type | CodeableConcept
Is Modifier | false
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
18. MolecularSequence.repository
Définition | Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
Short | External repository which contains detailed report related with observedSeq in this resource
Control | 10..*
Type | BackboneElement
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
Slicing | This element introduces a set of slices on `MolecularSequence.repository`. The slices areUnordered and Open, and can be differentiated using the following discriminators: pattern @ type
20. MolecularSequence.repository.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
22. MolecularSequence.repository.type
Définition | Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.
Short | directlink | openapi | login | oauth | other
Control | 1..1
Binding | The codes SHALL be taken from repositoryType http://hl7.org/fhir/ValueSet/repository-type|4.0.1 (required to `http://hl7.org/fhir/ValueSet/repository-type|4.0.1` ) Type for access of external URI.
Type | code
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
24. MolecularSequence.repository:reference-db
Nom de la slice | reference-db
Définition | Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
Short | External repository which contains detailed report related with observedSeq in this resource
Control | 10..1*
Type | BackboneElement
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
26. MolecularSequence.repository:reference-db.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
28. MolecularSequence.repository:reference-db.type
Définition | Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.
Short | directlink | openapi | login | oauth | other
Control | 1..1
Binding | The codes SHALL be taken from repositoryType http://hl7.org/fhir/ValueSet/repository-type|4.0.1 (required to `http://hl7.org/fhir/ValueSet/repository-type|4.0.1` ) Type for access of external URI.
Type | code
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Pattern Value | `other`
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
30. MolecularSequence.repository:reference-db.name
Définition | Reference database name URI of an external repository which contains further details about the genetics data.
Short | Reference database nameRepository's name
Control | 10..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
32. MolecularSequence.repository:reference-db.datasetId
Définition | Identifier of the annotation in the database 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.
Short | Identifier of the annotation in the databaseId of the dataset that used to call for dataset in repository
Control | 10..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
34. MolecularSequence.repository:pfam-domain
Nom de la slice | pfam-domain
Définition | Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
Short | External repository which contains detailed report related with observedSeq in this resource
Control | 0..1*
Type | BackboneElement
Is Modifier | false
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
36. MolecularSequence.repository:pfam-domain.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
38. MolecularSequence.repository:pfam-domain.type
Définition | Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.
Short | directlink | openapi | login | oauth | other
Control | 1..1
Binding | The codes SHALL be taken from repositoryType http://hl7.org/fhir/ValueSet/repository-type|4.0.1 (required to `http://hl7.org/fhir/ValueSet/repository-type|4.0.1` ) Type for access of external URI.
Type | code
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Pattern Value | `directlink`
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
40. MolecularSequence.repository:pfam-domain.url
Définition | URI of an external repository which contains further details about the genetics data.
Short | URI of the repository
Control | 0..1
Type | uri
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Pattern Value | `http://pfam.xfam.org/`
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
42. MolecularSequence.repository:pfam-domain.name
Définition | URI of an external repository which contains further details about the genetics data.
Short | Repository's name
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Pattern Value | `pfam`
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
44. MolecularSequence.repository:pfam-domain.datasetId
Définition | Identifier in the database of protein families and protein domains (Pfam) containing the genetic alteration. 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.
Short | Pfam IDId of the dataset that used to call for dataset in repository
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
46. MolecularSequence.repository:pfam-domain.readsetId
Définition | Name of the protein domain in the Pfam database containing the genetic alteration. Id of the read in this external repository.
Short | Pfam domain nameId of the read
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))

Guidance on how to interpret the contents of this table can be found here

0. MolecularSequence
2. MolecularSequence.coordinateSystem
Pattern Value | `0`
4. MolecularSequence.patient
Type | Reference(Oncology Patient)
Must Support | true
6. MolecularSequence.referenceSeq
8. MolecularSequence.referenceSeq.orientation
Définition | Strand orientation of the annotation DNA
Short | DNA strand orientation
Must Support | true
10. MolecularSequence.referenceSeq.referenceSeqId
Définition | Type of the annotation referenced to describe the molecular entity
Short | Type of the referenced annotation
Control | 1..?
Binding | Unless not suitable, these codes SHALL be taken from Reference Type Value Set (extensible to `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/ReferenceType` )
Must Support | true
12. MolecularSequence.repository
Control | 1..?
Slicing | This element introduces a set of slices on `MolecularSequence.repository`. The slices areUnordered and Open, and can be differentiated using the following discriminators: pattern @ type
14. MolecularSequence.repository:reference-db
Nom de la slice | reference-db
Control | 1..1
16. MolecularSequence.repository:reference-db.type
Pattern Value | `other`
18. MolecularSequence.repository:reference-db.name
Définition | Reference database name
Short | Reference database name
Control | 1..?
Must Support | true
20. MolecularSequence.repository:reference-db.datasetId
Définition | Identifier of the annotation in the database
Short | Identifier of the annotation in the database
Control | 1..?
Must Support | true
22. MolecularSequence.repository:pfam-domain
Nom de la slice | pfam-domain
Control | 0..1
Must Support | true
24. MolecularSequence.repository:pfam-domain.type
Pattern Value | `directlink`
26. MolecularSequence.repository:pfam-domain.url
Pattern Value | `http://pfam.xfam.org/`
28. MolecularSequence.repository:pfam-domain.name
Pattern Value | `pfam`
30. MolecularSequence.repository:pfam-domain.datasetId
Définition | Identifier in the database of protein families and protein domains (Pfam) containing the genetic alteration.
Short | Pfam ID
Must Support | true
32. MolecularSequence.repository:pfam-domain.readsetId
Définition | Name of the protein domain in the Pfam database containing the genetic alteration.
Short | Pfam domain name
Must Support | true

Guidance on how to interpret the contents of this table can be found here

0. MolecularSequence
Définition | Raw data describing a biological sequence.
Short | Information about a biological sequence
Control | 0..*
Is Modifier | false
Résumé | false
Invariants | dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources (`contained.contained.empty()`) dom-3: If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource (`contained.where((('#'+id 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()`) dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated (`contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()`) dom-5: If a resource is contained in another resource, it SHALL NOT have a security label (`contained.meta.security.empty()`) dom-6: A resource should have narrative for robust management (`text.`div`.exists()`) msq-3: Only 0 and 1 are valid for coordinateSystem (`coordinateSystem = 1 or coordinateSystem = 0`)
2. MolecularSequence.id
Définition | The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
Short | Logical id of this artifact
Commentaires | The only time that a resource does not have an id is when it is being submitted to the server using a create operation.
Control | 0..1
Type | id
Is Modifier | false
Résumé | true
4. MolecularSequence.meta
Définition | 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.
Short | Metadata about the resource
Control | 0..1
Type | Meta
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
6. MolecularSequence.implicitRules
Définition | 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.
Short | A set of rules under which this content was created
Commentaires | 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.
Control | 0..1
Type | uri
Is Modifier | true because 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
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
8. MolecularSequence.language
Définition | The base language in which the resource is written.
Short | Language of the resource content
Commentaires | 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).
Control | 0..1
Binding | The codes SHOULD be taken from CommonLanguages (preferred to `http://hl7.org/fhir/ValueSet/languages` ) A human language.
Bindings Additionnels | But
AllLanguages | Binding Max
Type | code
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
10. MolecularSequence.text
Définition | 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.
Short | Text summary of the resource, for human interpretation
Commentaires | 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.
Control | 0..1
Type | Narrative
Is Modifier | false
Résumé | false
Alternate Names | narrative, html, xhtml, display
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
12. MolecularSequence.contained
Définition | 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.
Short | Contained, inline Resources
Commentaires | 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.
Control | 0..*
Type | Resource
Is Modifier | false
Résumé | false
Alternate Names | inline resources, anonymous resources, contained resources
14. MolecularSequence.extension
Définition | 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.
Short | Additional content defined by implementations
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | false
Résumé | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
16. MolecularSequence.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
Résumé | false
Requirements | 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.
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
18. MolecularSequence.identifier
Définition | A unique identifier for this particular sequence instance. This is a FHIR-defined id.
Short | Unique ID for this particular sequence. This is a FHIR-defined id
Note | This is a business identifier, not a resource identifier (see discussion)
Control | 0..*
Type | Identifier
Is Modifier | false
Résumé | true
Requirements | Allows sequences to be distinguished and referenced.
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
20. MolecularSequence.type
Définition | Amino Acid Sequence/ DNA Sequence / RNA Sequence.
Short | aa | dna | rna
Control | 0..1
Binding | The codes SHALL be taken from sequenceType (required to `http://hl7.org/fhir/ValueSet/sequence-type|4.0.1` ) Type if a sequence -- DNA, RNA, or amino acid sequence.
Type | code
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
22. MolecularSequence.coordinateSystem
Définition | 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).
Short | 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)
Control | 1..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Pattern Value | `0`
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
24. MolecularSequence.patient
Définition | The patient whose sequencing results are described by this resource.
Short | Who and/or what this is about
Control | 0..1
Type | Reference(Oncology Patient)
Is Modifier | false
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
26. MolecularSequence.specimen
Définition | Specimen used for sequencing.
Short | Specimen used for sequencing
Control | 0..1
Type | Reference(Specimen)
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
28. MolecularSequence.device
Définition | The method for sequencing, for example, chip information.
Short | The method for sequencing
Control | 0..1
Type | Reference(Device)
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
30. MolecularSequence.performer
Définition | The organization or lab that should be responsible for this result.
Short | Who should be responsible for test result
Control | 0..1
Type | Reference(Organization)
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
32. MolecularSequence.quantity
Définition | The number of copies of the sequence of interest. (RNASeq).
Short | The number of copies of the sequence of interest. (RNASeq)
Control | 0..1
Type | Quantity
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
34. MolecularSequence.referenceSeq
Définition | A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
Short | A sequence used as reference
Control | 0..1
Type | BackboneElement
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained (`(chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())`) msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString; (`(genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1`)
36. MolecularSequence.referenceSeq.id
Définition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short | Unique id for inter-element referencing
Control | 0..1
Type | string
Is Modifier | false
XML Format | In the XML format, this property is represented as an attribute.
Résumé | false
38. MolecularSequence.referenceSeq.extension
Définition | 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.
Short | Additional content defined by implementations
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | false
Résumé | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
40. MolecularSequence.referenceSeq.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
42. MolecularSequence.referenceSeq.chromosome
Définition | 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).
Short | Chromosome containing genetic finding
Control | 0..1
Binding | For example codes, see chromosome-human (example to `http://hl7.org/fhir/ValueSet/chromosome-human` ) Chromosome number for human.
Type | CodeableConcept
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
44. MolecularSequence.referenceSeq.genomeBuild
Définition | 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.
Short | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
46. MolecularSequence.referenceSeq.orientation
Définition | Strand orientation of the annotation DNA
Short | DNA strand orientation
Control | 0..1
Binding | The codes SHALL be taken from orientationType (required to `http://hl7.org/fhir/ValueSet/orientation-type|4.0.1` ) Type for orientation.
Type | code
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
48. MolecularSequence.referenceSeq.referenceSeqId
Définition | Type of the annotation referenced to describe the molecular entity
Short | Type of the referenced annotation
Control | 1..1
Binding | Unless not suitable, these codes SHALL be taken from Reference Type Value Set (extensible to `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/ReferenceType` )
Type | CodeableConcept
Is Modifier | false
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
50. MolecularSequence.referenceSeq.referenceSeqPointer
Définition | A pointer to another MolecularSequence entity as reference sequence.
Short | A pointer to another MolecularSequence entity as reference sequence
Control | 0..1
Type | Reference(MolecularSequence)
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
52. MolecularSequence.referenceSeq.referenceSeqString
Définition | A string like "ACGT".
Short | A string to represent reference sequence
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
54. MolecularSequence.referenceSeq.strand
Définition | 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.
Short | watson | crick
Control | 0..1
Binding | The codes SHALL be taken from strandType (required to `http://hl7.org/fhir/ValueSet/strand-type|4.0.1` ) Type for strand.
Type | code
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
56. MolecularSequence.referenceSeq.windowStart
Définition | 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.
Short | Start position of the window on the reference sequence
Control | 0..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
58. MolecularSequence.referenceSeq.windowEnd
Définition | 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.
Short | End position of the window on the reference sequence
Control | 0..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
60. MolecularSequence.variant
Définition | The definition of variant here originates from Sequence ontology (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.
Short | Variant in sequence
Control | 0..*
Type | BackboneElement
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
62. MolecularSequence.variant.id
Définition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short | Unique id for inter-element referencing
Control | 0..1
Type | string
Is Modifier | false
XML Format | In the XML format, this property is represented as an attribute.
Résumé | false
64. MolecularSequence.variant.extension
Définition | 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.
Short | Additional content defined by implementations
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | false
Résumé | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
66. MolecularSequence.variant.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
68. MolecularSequence.variant.start
Définition | 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.
Short | Start position of the variant on the reference sequence
Control | 0..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
70. MolecularSequence.variant.end
Définition | 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.
Short | End position of the variant on the reference sequence
Control | 0..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
72. MolecularSequence.variant.observedAllele
Définition | An allele is one of a set of coexisting sequence variants of a gene (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.
Short | Allele that was observed
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
74. MolecularSequence.variant.referenceAllele
Définition | An allele is one of a set of coexisting sequence variants of a gene (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.
Short | Allele in the reference sequence
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
76. MolecularSequence.variant.cigar
Définition | Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation here.
Short | Extended CIGAR string for aligning the sequence with reference bases
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
78. MolecularSequence.variant.variantPointer
Définition | A pointer to an Observation containing variant information.
Short | Pointer to observed variant information
Control | 0..1
Type | Reference(Observation)
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
80. MolecularSequence.observedSeq
Définition | 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.
Short | Sequence that was observed
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
82. MolecularSequence.quality
Définition | An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score (SO:0001686).
Short | An set of value as quality of sequence
Control | 0..*
Type | BackboneElement
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
84. MolecularSequence.quality.id
Définition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short | Unique id for inter-element referencing
Control | 0..1
Type | string
Is Modifier | false
XML Format | In the XML format, this property is represented as an attribute.
Résumé | false
86. MolecularSequence.quality.extension
Définition | 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.
Short | Additional content defined by implementations
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | false
Résumé | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
88. MolecularSequence.quality.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
90. MolecularSequence.quality.type
Définition | INDEL / SNP / Undefined variant.
Short | indel | snp | unknown
Control | 1..1
Binding | The codes SHALL be taken from qualityType (required to `http://hl7.org/fhir/ValueSet/quality-type|4.0.1` ) Type for quality report.
Type | code
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
92. MolecularSequence.quality.standardSequence
Définition | Gold standard sequence used for comparing against.
Short | Standard sequence for comparison
Control | 0..1
Binding | For example codes, see FDA-StandardSequence (example to `http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence` ) Reference identifier of the sequence that used to mark the quality of tested samples.
Type | CodeableConcept
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
94. MolecularSequence.quality.start
Définition | Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
Short | Start position of the sequence
Control | 0..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
96. MolecularSequence.quality.end
Définition | 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.
Short | End position of the sequence
Control | 0..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
98. MolecularSequence.quality.score
Définition | The score of an experimentally derived feature such as a p-value (SO:0001685).
Short | Quality score for the comparison
Control | 0..1
Type | Quantity
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
100. MolecularSequence.quality.method
Définition | Which method is used to get sequence quality.
Short | Method to get quality
Control | 0..1
Binding | For example codes, see FDA-Method (example to `http://hl7.org/fhir/ValueSet/sequence-quality-method` ) The method used to evaluate the numerical quality of the observed sequence.
Type | CodeableConcept
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
102. MolecularSequence.quality.truthTP
Définition | 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.
Short | True positives from the perspective of the truth data
Control | 0..1
Type | decimal
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
104. MolecularSequence.quality.queryTP
Définition | 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.
Short | True positives from the perspective of the query data
Control | 0..1
Type | decimal
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
106. MolecularSequence.quality.truthFN
Définition | 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.
Short | False negatives
Control | 0..1
Type | decimal
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
108. MolecularSequence.quality.queryFP
Définition | 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.
Short | False positives
Control | 0..1
Type | decimal
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
110. MolecularSequence.quality.gtFP
Définition | 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).
Short | False positives where the non-REF alleles in the Truth and Query Call Sets match
Control | 0..1
Type | decimal
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
112. MolecularSequence.quality.precision
Définition | QUERY.TP / (QUERY.TP + QUERY.FP).
Short | Precision of comparison
Control | 0..1
Type | decimal
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
114. MolecularSequence.quality.recall
Définition | TRUTH.TP / (TRUTH.TP + TRUTH.FN).
Short | Recall of comparison
Control | 0..1
Type | decimal
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
116. MolecularSequence.quality.fScore
Définition | Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
Short | F-score
Control | 0..1
Type | decimal
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
118. MolecularSequence.quality.roc
Définition | Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.
Short | Receiver Operator Characteristic (ROC) Curve
Control | 0..1
Type | BackboneElement
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
120. MolecularSequence.quality.roc.id
Définition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short | Unique id for inter-element referencing
Control | 0..1
Type | string
Is Modifier | false
XML Format | In the XML format, this property is represented as an attribute.
Résumé | false
122. MolecularSequence.quality.roc.extension
Définition | 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.
Short | Additional content defined by implementations
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | false
Résumé | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
124. MolecularSequence.quality.roc.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
126. MolecularSequence.quality.roc.score
Définition | Invidual data point representing the GQ (genotype quality) score threshold.
Short | Genotype quality score
Control | 0..*
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
128. MolecularSequence.quality.roc.numTP
Définition | The number of true positives if the GQ score threshold was set to "score" field value.
Short | Roc score true positive numbers
Control | 0..*
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
130. MolecularSequence.quality.roc.numFP
Définition | The number of false positives if the GQ score threshold was set to "score" field value.
Short | Roc score false positive numbers
Control | 0..*
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
132. MolecularSequence.quality.roc.numFN
Définition | The number of false negatives if the GQ score threshold was set to "score" field value.
Short | Roc score false negative numbers
Control | 0..*
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
134. MolecularSequence.quality.roc.precision
Définition | Calculated precision if the GQ score threshold was set to "score" field value.
Short | Precision of the GQ score
Control | 0..*
Type | decimal
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
136. MolecularSequence.quality.roc.sensitivity
Définition | Calculated sensitivity if the GQ score threshold was set to "score" field value.
Short | Sensitivity of the GQ score
Control | 0..*
Type | decimal
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
138. MolecularSequence.quality.roc.fMeasure
Définition | Calculated fScore if the GQ score threshold was set to "score" field value.
Short | FScore of the GQ score
Control | 0..*
Type | decimal
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
140. MolecularSequence.readCoverage
Définition | Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
Short | Average number of reads representing a given nucleotide in the reconstructed sequence
Control | 0..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
142. MolecularSequence.repository
Définition | Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
Short | External repository which contains detailed report related with observedSeq in this resource
Control | 1..*
Type | BackboneElement
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
Slicing | This element introduces a set of slices on `MolecularSequence.repository`. The slices areUnordered and Open, and can be differentiated using the following discriminators: pattern @ type
144. MolecularSequence.repository.id
Définition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short | Unique id for inter-element referencing
Control | 0..1
Type | string
Is Modifier | false
XML Format | In the XML format, this property is represented as an attribute.
Résumé | false
146. MolecularSequence.repository.extension
Définition | 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.
Short | Additional content defined by implementations
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | false
Résumé | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
148. MolecularSequence.repository.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
150. MolecularSequence.repository.type
Définition | Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.
Short | directlink | openapi | login | oauth | other
Control | 1..1
Binding | The codes SHALL be taken from repositoryType (required to `http://hl7.org/fhir/ValueSet/repository-type|4.0.1` ) Type for access of external URI.
Type | code
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
152. MolecularSequence.repository.url
Définition | URI of an external repository which contains further details about the genetics data.
Short | URI of the repository
Control | 0..1
Type | uri
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
154. MolecularSequence.repository.name
Définition | URI of an external repository which contains further details about the genetics data.
Short | Repository's name
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
156. MolecularSequence.repository.datasetId
Définition | 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.
Short | Id of the dataset that used to call for dataset in repository
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
158. MolecularSequence.repository.variantsetId
Définition | 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.
Short | Id of the variantset that used to call for variantset in repository
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
160. MolecularSequence.repository.readsetId
Définition | Id of the read in this external repository.
Short | Id of the read
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
162. MolecularSequence.repository:reference-db
Nom de la slice | reference-db
Définition | Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
Short | External repository which contains detailed report related with observedSeq in this resource
Control | 1..1
Type | BackboneElement
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
164. MolecularSequence.repository:reference-db.id
Définition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short | Unique id for inter-element referencing
Control | 0..1
Type | string
Is Modifier | false
XML Format | In the XML format, this property is represented as an attribute.
Résumé | false
166. MolecularSequence.repository:reference-db.extension
Définition | 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.
Short | Additional content defined by implementations
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | false
Résumé | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
168. MolecularSequence.repository:reference-db.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
170. MolecularSequence.repository:reference-db.type
Définition | Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.
Short | directlink | openapi | login | oauth | other
Control | 1..1
Binding | The codes SHALL be taken from repositoryType (required to `http://hl7.org/fhir/ValueSet/repository-type|4.0.1` ) Type for access of external URI.
Type | code
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Pattern Value | `other`
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
172. MolecularSequence.repository:reference-db.url
Définition | URI of an external repository which contains further details about the genetics data.
Short | URI of the repository
Control | 0..1
Type | uri
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
174. MolecularSequence.repository:reference-db.name
Définition | Reference database name
Short | Reference database name
Control | 1..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
176. MolecularSequence.repository:reference-db.datasetId
Définition | Identifier of the annotation in the database
Short | Identifier of the annotation in the database
Control | 1..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
178. MolecularSequence.repository:reference-db.variantsetId
Définition | 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.
Short | Id of the variantset that used to call for variantset in repository
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
180. MolecularSequence.repository:reference-db.readsetId
Définition | Id of the read in this external repository.
Short | Id of the read
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
182. MolecularSequence.repository:pfam-domain
Nom de la slice | pfam-domain
Définition | Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
Short | External repository which contains detailed report related with observedSeq in this resource
Control | 0..1
Type | BackboneElement
Is Modifier | false
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
184. MolecularSequence.repository:pfam-domain.id
Définition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short | Unique id for inter-element referencing
Control | 0..1
Type | string
Is Modifier | false
XML Format | In the XML format, this property is represented as an attribute.
Résumé | false
186. MolecularSequence.repository:pfam-domain.extension
Définition | 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.
Short | Additional content defined by implementations
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | false
Résumé | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
188. MolecularSequence.repository:pfam-domain.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
190. MolecularSequence.repository:pfam-domain.type
Définition | Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.
Short | directlink | openapi | login | oauth | other
Control | 1..1
Binding | The codes SHALL be taken from repositoryType (required to `http://hl7.org/fhir/ValueSet/repository-type|4.0.1` ) Type for access of external URI.
Type | code
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Pattern Value | `directlink`
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
192. MolecularSequence.repository:pfam-domain.url
Définition | URI of an external repository which contains further details about the genetics data.
Short | URI of the repository
Control | 0..1
Type | uri
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Pattern Value | `http://pfam.xfam.org/`
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
194. MolecularSequence.repository:pfam-domain.name
Définition | URI of an external repository which contains further details about the genetics data.
Short | Repository's name
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Pattern Value | `pfam`
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
196. MolecularSequence.repository:pfam-domain.datasetId
Définition | Identifier in the database of protein families and protein domains (Pfam) containing the genetic alteration.
Short | Pfam ID
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
198. MolecularSequence.repository:pfam-domain.variantsetId
Définition | 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.
Short | Id of the variantset that used to call for variantset in repository
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
200. MolecularSequence.repository:pfam-domain.readsetId
Définition | Name of the protein domain in the Pfam database containing the genetic alteration.
Short | Pfam domain name
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Must Support | true
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
202. MolecularSequence.pointer
Définition | Pointer to next atomic sequence which at most contains one variant.
Short | Pointer to next atomic sequence
Control | 0..*
Type | Reference(MolecularSequence)
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
204. MolecularSequence.structureVariant
Définition | Information about chromosome structure variation.
Short | Structural variant
Control | 0..*
Type | BackboneElement
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
206. MolecularSequence.structureVariant.id
Définition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short | Unique id for inter-element referencing
Control | 0..1
Type | string
Is Modifier | false
XML Format | In the XML format, this property is represented as an attribute.
Résumé | false
208. MolecularSequence.structureVariant.extension
Définition | 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.
Short | Additional content defined by implementations
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | false
Résumé | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
210. MolecularSequence.structureVariant.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
212. MolecularSequence.structureVariant.variantType
Définition | Information about chromosome structure variation DNA change type.
Short | Structural variant change type
Control | 0..1
Binding | The codes SHALL be taken from LOINC Answer List LL379-9|4.0.1 (required to `http://loinc.org/vs/LL379-9|4.0.1` ) DNA change type.
Type | CodeableConcept
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
214. MolecularSequence.structureVariant.exact
Définition | Used to indicate if the outer and inner start-end values have the same meaning.
Short | Does the structural variant have base pair resolution breakpoints?
Control | 0..1
Type | boolean
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
216. MolecularSequence.structureVariant.length
Définition | Length of the variant chromosome.
Short | Structural variant length
Control | 0..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
218. MolecularSequence.structureVariant.outer
Définition | Structural variant outer.
Short | Structural variant outer
Control | 0..1
Type | BackboneElement
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
220. MolecularSequence.structureVariant.outer.id
Définition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short | Unique id for inter-element referencing
Control | 0..1
Type | string
Is Modifier | false
XML Format | In the XML format, this property is represented as an attribute.
Résumé | false
222. MolecularSequence.structureVariant.outer.extension
Définition | 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.
Short | Additional content defined by implementations
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | false
Résumé | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
224. MolecularSequence.structureVariant.outer.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
226. MolecularSequence.structureVariant.outer.start
Définition | Structural variant outer start. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
Short | Structural variant outer start
Control | 0..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
228. MolecularSequence.structureVariant.outer.end
Définition | 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.
Short | Structural variant outer end
Control | 0..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
230. MolecularSequence.structureVariant.inner
Définition | Structural variant inner.
Short | Structural variant inner
Control | 0..1
Type | BackboneElement
Is Modifier | false
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
232. MolecularSequence.structureVariant.inner.id
Définition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short | Unique id for inter-element referencing
Control | 0..1
Type | string
Is Modifier | false
XML Format | In the XML format, this property is represented as an attribute.
Résumé | false
234. MolecularSequence.structureVariant.inner.extension
Définition | 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.
Short | Additional content defined by implementations
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | false
Résumé | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
236. MolecularSequence.structureVariant.inner.modifierExtension
Définition | 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).
Short | Extensions that cannot be ignored even if unrecognized
Commentaires | 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Résumé | true
Requirements | 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.
Alternate Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
238. MolecularSequence.structureVariant.inner.start
Définition | Structural variant inner start. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
Short | Structural variant inner start
Control | 0..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
240. MolecularSequence.structureVariant.inner.end
Définition | 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.
Short | Structural variant inner end
Control | 0..1
Type | integer
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Résumé | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)