Implementierungsleitfaden für DEMIS Integrierte Genomische Surveillance (IGS)

There are no (further) constraints on this element

Element id

MolecularSequence.id

Short description

Logical id of this artifact

Definition

The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.

Comments

The only time that a resource does not have an id is when it is being submitted to the server using a create operation.

Data type

Meta

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
rim: N/A

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.meta.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

MolecularSequence.meta.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

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.

Comments

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.

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

versionId

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.meta.versionId

Short description

Version specific identifier

Definition

The version specific identifier, as it appears in the version portion of the URL. This value changes when the resource is created, updated, or deleted.

Comments

The server assigns this value, and ignores what the client specifies, except in the case that the server is imposing version integrity on updates/deletes.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

lastUpdated

0..1

instant

There are no (further) constraints on this element

Element id

MolecularSequence.meta.lastUpdated

Short description

When the resource version last changed

Definition

When the resource last changed - e.g. when the version changed.

Comments

This value is always populated except when the resource is first being created. The server / resource manager sets this value; what a client provides is irrelevant. This is equivalent to the HTTP Last-Modified and SHOULD have the same value on a read interaction.

Data type

instant

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

source

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.meta.source

Short description

Identifies where the resource comes from

Definition

A uri that identifies the source system of the resource. This provides a minimal amount of Provenance information that can be used to track or differentiate the source of information in the resource. The source may identify another FHIR server, document, message, database, etc.

Comments

In the provenance resource, this corresponds to Provenance.entity.what[x]. The exact use of the source (and the implied Provenance.entity.role) is left to implementer discretion. Only one nominated source is allowed; for additional provenance details, a full Provenance resource should be used.

This element can be used to indicate where the current master source of a resource that has a canonical URL if the resource is no longer hosted at the canonical URL.

Data type

canonical(StructureDefinition)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

profile

S Σ

1..1

canonical(StructureDefinition)Fixed Value

Element id

MolecularSequence.meta.profile

Short description

Profiles this resource claims to conform to

Definition

A list of profiles (references to StructureDefinition resources) that this resource claims to conform to. The URL is a reference to StructureDefinition.url.

Comments

It is up to the server and/or other infrastructure of policy to determine whether/how these claims are verified and/or updated over time. The list of profile URLs is a set.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Fixed value

https://demis.rki.de/fhir/igs/StructureDefinition/Sequence

Mappings

rim: n/a

security

0..*

CodingBinding

There are no (further) constraints on this element

Element id

MolecularSequence.meta.security

Short description

Security Labels applied to this resource

Definition

Security labels applied to this resource. These tags connect specific resources to the overall security policy and infrastructure.

Comments

The security labels can be updated without changing the stated version of the resource. The list of security labels is a set. Uniqueness is based the system/code, and version and display are ignored.

Data type

Coding

Binding

Security Labels from the Healthcare Privacy and Security Classification System.

All Security Labels (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE subset one of the sets of component 1-3 or 4-6
rim: CV
orim: fhir:Coding rdfs:subClassOf dt:CDCoding

tag

0..*

Coding

There are no (further) constraints on this element

Element id

MolecularSequence.meta.tag

Short description

Tags applied to this resource

Definition

Tags applied to this resource. Tags are intended to be used to identify and relate resources to process and workflow, and applications are not required to consider the tags when interpreting the meaning of a resource.

Comments

The tags can be updated without changing the stated version of the resource. The list of tags is a set. Uniqueness is based the system/code, and version and display are ignored.

Data type

Coding

Binding

Codes that represent various types of tags, commonly workflow-related; e.g. "Needs review by Dr. Jones".

CommonTags (example)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE subset one of the sets of component 1-3 or 4-6
rim: CV
orim: fhir:Coding rdfs:subClassOf dt:CDCoding

implicitRules

Σ ?!

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.implicitRules

Short description

A set of rules under which this content was created

Definition

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.

Comments

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.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

language

0..1

codeBinding

There are no (further) constraints on this element

Element id

MolecularSequence.language

Short description

Language of the resource content

Definition

The base language in which the resource is written.

Comments

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).

Data type

code

Binding

A human language.

CommonLanguages (preferred)

Binding extensions

maxValueSet	AllLanguages

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

text

0..1

Narrative

There are no (further) constraints on this element

Element id

MolecularSequence.text

Short description

Text summary of the resource, for human interpretation

Alternate names

narrative, html, xhtml, display

Definition

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.

Comments

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.

Data type

Narrative

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
rim: N/A
rim: Act.text?

contained

0..*

Resource

There are no (further) constraints on this element

Element id

MolecularSequence.contained

Short description

Contained, inline Resources

Alternate names

inline resources, anonymous resources, contained resources

Definition

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.

Comments

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.

Data type

Resource

Mappings

rim: Entity. Role, or Act
rim: N/A

extension

S C

1..*

Element id

MolecularSequence.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

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.

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

sequenceAuthor

S C

0..1

Element id

MolecularSequence.extension:sequenceAuthor

Short description

Person/Labor, die/das verantwortlich für die Sequenz ist

Alternate names

extensions, user content

Definition

Person/Labor, die/das verantwortlich für die Sequenz ist

Comments

Data type

https://demis.rki.de/fhir/igs/StructureDefinition/SequenceAuthor

Extension URL

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

sequencingReason

S C

0..1

Element id

MolecularSequence.extension:sequencingReason

Short description

Grund der Sequenzierung

Alternate names

extensions, user content

Definition

Grund der Sequenzierung

Comments

Data type

https://demis.rki.de/fhir/igs/StructureDefinition/SequencingReason

Extension URL

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

sequenceDocumentReference

S C

1..*

Extension(Reference(SequenceDocument))

Element id

MolecularSequence.extension:sequenceDocumentReference

Short description

Referenz auf die Sequenz

Alternate names

extensions, user content

Definition

Referenz auf die Sequenz

Comments

Data type

Extension(Reference(SequenceDocument))

Extension URL

https://demis.rki.de/fhir/igs/StructureDefinition/SequenceDocumentReference

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

modifierExtension

?! C

0..*

There are no (further) constraints on this element

Element id

MolecularSequence.modifierExtension

Short description

Extensions that cannot be ignored

Alternate names

extensions, user content

Definition

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).

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.

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

identifier

S Σ

1..1

Element id

MolecularSequence.identifier

Short description

Laboreigener Identifier der Probe

Definition

Eineindeutiger Identifier der Probe, die vom einreichenden Labor verwendet wird.

Requirements

Allows sequences to be distinguished and referenced.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CX / EI (occasionally, more often EI maps to a resource id or a URL)
rim: II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT]
servd: Identifier
w5: FiveWs.identifier

type

S Σ

0..1

codeBindingFixed Value

Element id

MolecularSequence.type

Short description

Typ der Sequenz

Definition

Für DEMIS ist der Typ grundsätzlich mit dem Wert „dna“ zu belegen.

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Data type

code

Binding

Type if a sequence -- DNA, RNA, or amino acid sequence.

sequenceType (required)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Fixed value

dna

Mappings

rim: n/a

coordinateSystem

1..1

There are no (further) constraints on this element

Element id

MolecularSequence.coordinateSystem

Short description

Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)

Definition

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).

Comments

32 bit number; for values larger than this, use decimal

Data type

Reference(SpecimenSequence)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

patient

Σ C

0..0

Reference(Patient)

There are no (further) constraints on this element

Element id

MolecularSequence.patient

Short description

Who and/or what this is about

Definition

The patient whose sequencing results are described by this resource.

Comments

References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository.

Data type

Reference(Patient)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ref-1: SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))

Mappings

rim: n/a
rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity)

specimen

S Σ C

1..1

Element id

MolecularSequence.specimen

Short description

Verweis auf die Sequenz-Probe

Definition

Verweis auf die Sequenz-Probe

Comments

Data type

Reference(SpecimenSequence)

Allowed aggregation:bundled

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ref-1: SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))

Mappings

rim: n/a
rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity)

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.specimen.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

MolecularSequence.specimen.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

reference

S Σ C

1..1

There are no (further) constraints on this element

Element id

MolecularSequence.specimen.reference

Short description

Literal reference, Relative, internal or absolute URL

Definition

A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.

Comments

Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure "/[type]/[id]" then it should be assumed that the reference is to a FHIR RESTful server.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, ref-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
rim: N/A

type

0..1

uriBinding

There are no (further) constraints on this element

Element id

MolecularSequence.specimen.type

Short description

Type the reference refers to (e.g. "Patient")

Definition

The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.

The type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. "Patient" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).

Comments

This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified.

Data type

Binding

Aa resource (or, for logical models, the URI of the logical model).

ResourceType (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
rim: N/A

identifier

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.specimen.identifier

Short description

Logical reference, when literal reference is not known

Definition

An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.

Comments

When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy.

When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference

Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.

Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any).

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CX / EI (occasionally, more often EI maps to a resource id or a URL)
rim: II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT]
servd: Identifier
rim: .identifier

display

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.specimen.display

Short description

Text alternative for the resource

Definition

Plain text narrative that identifies the resource in addition to the resource reference.

Comments

This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.

Data type

Reference(SequencingDevice)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
rim: N/A

device

S Σ C

1..1

Element id

MolecularSequence.device

Short description

Verweis auf das Sequenziergerät

Definition

Verweis auf das Sequenziergerät

Comments

Data type

Reference(SequencingDevice)

Allowed aggregation:bundled

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ref-1: SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))

Mappings

rim: n/a
rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity)

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.device.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

MolecularSequence.device.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

reference

S Σ C

1..1

There are no (further) constraints on this element

Element id

MolecularSequence.device.reference

Short description

Literal reference, Relative, internal or absolute URL

Definition

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, ref-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
rim: N/A

type

0..1

uriBinding

There are no (further) constraints on this element

Element id

MolecularSequence.device.type

Short description

Type the reference refers to (e.g. "Patient")

Definition

The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.

Comments

Data type

Binding

Aa resource (or, for logical models, the URI of the logical model).

ResourceType (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
rim: N/A

identifier

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.device.identifier

Short description

Logical reference, when literal reference is not known

Definition

Comments

Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CX / EI (occasionally, more often EI maps to a resource id or a URL)
rim: II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT]
servd: Identifier
rim: .identifier

display

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.device.display

Short description

Text alternative for the resource

Definition

Plain text narrative that identifies the resource in addition to the resource reference.

Comments

This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.

Data type

Reference(NotifierFacility)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
rim: N/A

performer

S Σ C

1..1

Element id

MolecularSequence.performer

Short description

Verweis auf die Melder-Einrichtung

Definition

Verweis auf die Melder-Einrichtung

Comments

Data type

Reference(NotifierFacility)

Allowed aggregation:bundled

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ref-1: SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))

Mappings

rim: n/a
rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity)

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.performer.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

MolecularSequence.performer.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

reference

S Σ C

1..1

There are no (further) constraints on this element

Element id

MolecularSequence.performer.reference

Short description

Literal reference, Relative, internal or absolute URL

Definition

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, ref-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
rim: N/A

type

0..1

uriBinding

There are no (further) constraints on this element

Element id

MolecularSequence.performer.type

Short description

Type the reference refers to (e.g. "Patient")

Definition

The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent.

Comments

Data type

Binding

Aa resource (or, for logical models, the URI of the logical model).

ResourceType (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
rim: N/A

identifier

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.performer.identifier

Short description

Logical reference, when literal reference is not known

Definition

Comments

Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CX / EI (occasionally, more often EI maps to a resource id or a URL)
rim: II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT]
servd: Identifier
rim: .identifier

display

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.performer.display

Short description

Text alternative for the resource

Definition

Plain text narrative that identifies the resource in addition to the resource reference.

Comments

This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
rim: N/A

quantity

Σ C

0..0

Quantity

There are no (further) constraints on this element

Element id

MolecularSequence.quantity

Short description

The number of copies of the sequence of interest. (RNASeq)

Definition

The number of copies of the sequence of interest. (RNASeq).

Comments

The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.

Data type

Quantity

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
qty-3: If a code for the unit is present, the system SHALL also be present
code.empty() or system.exists()

Mappings

rim: n/a
v2: SN (see also Range) or CQ
rim: PQ, IVL<PQ>, MO, CO, depending on the values

referenceSeq

Σ C

0..0

There are no (further) constraints on this element

Element id

MolecularSequence.referenceSeq

Short description

A sequence used as reference

Definition

A sequence that is used as a reference to describe variants that are present in a sequence analyzed.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
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())

Mappings

rim: n/a

variant

0..0

There are no (further) constraints on this element

Element id

MolecularSequence.variant

Short description

Variant in sequence

Definition

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.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

observedSeq

0..0

There are no (further) constraints on this element

Element id

MolecularSequence.observedSeq

Short description

Sequence that was observed

Definition

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.

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

quality

0..0

There are no (further) constraints on this element

Element id

MolecularSequence.quality

Short description

An set of value as quality of sequence

Definition

An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score (SO:0001686).

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

readCoverage

0..0

There are no (further) constraints on this element

Element id

MolecularSequence.readCoverage

Short description

Average number of reads representing a given nucleotide in the reconstructed sequence

Definition

Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.

Comments

32 bit number; for values larger than this, use decimal

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

repository

S Σ

0..*

Element id

MolecularSequence.repository

Short description

Repositorium, in welches die Sequenz hochgeladen wird

Definition

Repositorium, in welches die Sequenz hochgeladen wird

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.repository.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

S C

1..*

Element id

MolecularSequence.repository.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

https://demis.rki.de/fhir/igs/StructureDefinition/SequenceUploadDate

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

sequenceUploadDate

S C

0..1

Extension(dateTime)

Element id

MolecularSequence.repository.extension:sequenceUploadDate

Short description

Datum des Sequenz-Uploads

Alternate names

extensions, user content

Definition

Datum des Sequenz-Uploads

Comments

Data type

Extension(dateTime)

Extension URL

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

sequenceUploadSubmitter

S C

0..1

Element id

MolecularSequence.repository.extension:sequenceUploadSubmitter

Short description

Verantwortliche/es Person/Labor für den Sequenz-Upload

Alternate names

extensions, user content

Definition

Verantwortliche/es Person/Labor für den Sequenz-Upload.

Comments

Data type

https://demis.rki.de/fhir/igs/StructureDefinition/SequenceUploadSubmitter

Extension URL

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

sequenceUploadStatus

S C

1..1

Element id

MolecularSequence.repository.extension:sequenceUploadStatus

Short description

Status des Sequenz-Uploads

Alternate names

extensions, user content

Definition

Status des Sequenz-Uploads.

Comments

Data type

https://demis.rki.de/fhir/igs/StructureDefinition/SequenceUploadStatus

Extension URL

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

MolecularSequence.repository.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

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).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

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()

Mappings

rim: n/a
rim: N/A

type

1..1

codeBinding

There are no (further) constraints on this element

Element id

MolecularSequence.repository.type

Short description

directlink | openapi | login | oauth | other

Definition

Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Data type

code

Binding

Type for access of external URI.

repositoryType (required)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

url

S Σ

0..1

Element id

MolecularSequence.repository.url

Short description

Hyperlink auf die Sequenz im Repositorium

Definition

Hyperlink auf die Sequenz im Repositorium.

Comments

see http://en.wikipedia.org/wiki/Uniform_resource_identifier

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

name

S Σ

1..1

stringBinding

Element id

MolecularSequence.repository.name

Short description

Name des Repositoriums

Definition

Name des Repositoriums, in welches die Sequenz hochgeladen wird. Der Wert muss entsprechend des vom RKI definierten ValueSets https://demis.rki.de/fhir/igs/ValueSet/repositoryName dargestellt werden.

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Data type

Binding

RepositoryName (required)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

datasetId

S Σ

0..1

Element id

MolecularSequence.repository.datasetId

Short description

Identifier der Sequenz im Repositorium

Definition

Identifier der Sequenz im Repositorium.

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

variantsetId

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.repository.variantsetId

Short description

Id of the variantset that used to call for variantset in repository

Definition

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.

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

readsetId

0..1

There are no (further) constraints on this element

Element id

MolecularSequence.repository.readsetId

Short description

Id of the read

Definition

Id of the read in this external repository.

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Data type

Reference(MolecularSequence)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a

pointer

Σ C

0..0

There are no (further) constraints on this element

Element id

MolecularSequence.pointer

Short description

Pointer to next atomic sequence

Definition

Pointer to next atomic sequence which at most contains one variant.

Comments

Data type

Reference(MolecularSequence)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ref-1: SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))

Mappings

rim: n/a
rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity)

structureVariant

0..0

There are no (further) constraints on this element

Element id

MolecularSequence.structureVariant

Short description

Structural variant

Definition

Information about chromosome structure variation.

Data type