NAPKON Pediatrics Module
1.0.0 - trial-use

NAPKON Pediatrics Module - Local Development build (v1.0.0). See the Directory of published versions

Resource Profile: SARS-CoV-2 RT PCR Specimen

Defining URL:https://www.napkon.de/fhir/StructureDefinition/sars-cov2-rt-pcr-specimen
Version:1.0.0
Name:SarsCoV2RTPCRSpecimen
Title:SARS-CoV-2 RT PCR Specimen
Status:Active as of 2021-11-09
Definition:

Qualitative detection of SARS-CoV-2 in specimens by RT-PCR

Publisher:Charité - Universitätsmedizin Berlin
Source Resource:XML / JSON / Turtle

The official URL for this profile is: 

https://www.napkon.de/fhir/StructureDefinition/sars-cov2-rt-pcr-specimen

Guidance

Parameter Case Report Form FHIR Resource Attribute
SARS-CoV-2 RT PCR in excreta Observation.valueCodeableConcept
Response Option Code
Detected Detected (qualifier value)
Not detected Not detected (qualifier value)
Inconclusive Inconclusive (qualifier value)

This profile is akin to the GECCO SARS-CoV-2-RT-PCR profile, but for excreta specimens, not respiratory specimens. The exact type of specimen is specified using the Observation.specimen attribute with a reference to the Specimen Excreta profile.

This profile of a FHIR Observation is derived from the ObservationLab profile of the Medical Informatics Initiative (MII).

Formal Views of Profile Content

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

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*ProfileObservationLaboruntersuchungMeasurements and simple assertions
... id SΣ0..1stringLogical id of this artifact
... meta SΣ0..1MetaMetadata about the resource
.... id 0..1stringUnique id for inter-element referencing
.... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... versionId Σ0..1idVersion specific identifier
.... lastUpdated Σ0..1instantWhen the resource version last changed
.... source SΣ0..1uriIdentifies where the resource comes from
.... profile SΣ0..*canonical(StructureDefinition)Profiles this resource claims to conform to
.... security Σ0..*CodingSecurity Labels applied to this resource
Binding: All Security Labels (extensible): Security Labels from the Healthcare Privacy and Security Classification System.


.... tag Σ0..*CodingTags applied to this resource
Binding: CommonTags (example): Codes that represent various types of tags, commonly workflow-related; e.g. "Needs review by Dr. Jones".


... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages: A human language.

... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
... Slices for modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
Slice: Unordered, Open by value:url
... Slices for identifier SΣ1..*IdentifierBusiness Identifier for observation
Slice: Unordered, Open by pattern:type
.... identifier:analyseBefundCode SΣ1..1IdentifierBusiness Identifier for observation
..... id 0..1stringUnique id for inter-element referencing
..... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... use ?!Σ0..1codeusual | official | temp | secondary | old (If known)
Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known .

..... type SΣ1..1CodeableConceptDescription of identifier
Binding: Identifier Type Codes (extensible): A coded type for an identifier that can be used to determine which identifier to use for a specific purpose.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0203
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: OBI
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
...... id 0..1stringUnique id for inter-element referencing
...... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... Slices for coding SΣ1..*CodingCode defined by a terminology system
Slice: Unordered, Open by value:system
....... coding:observationInstanceV2 SΣ1..1CodingCode defined by a terminology system
........ id 0..1stringUnique id for inter-element referencing
........ Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
........ system SΣ1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0203
........ version Σ0..1stringVersion of the system - if relevant
........ code SΣ1..1codeSymbol in syntax defined by the system
Fixed Value: OBI
........ display Σ0..1stringRepresentation defined by the system
........ userSelected Σ0..1booleanIf this coding was chosen directly by the user
...... text Σ0..1stringPlain text representation of the concept
..... system SΣ1..1uriThe namespace for the identifier value
Example General: http://www.acme.com/identifiers/patient
..... value SΣ1..1stringThe value that is unique
Example General: 123456
..... period ΣI0..1PeriodTime period when id is/was valid for use
..... assigner SΣI1..1Reference(Organization)A reference from one resource to another
... basedOn ΣI0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf ΣI0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... category S1..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... id 0..1stringUnique id for inter-element referencing
.... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... Slices for coding SΣ2..*CodingCode defined by a terminology system
Slice: Unordered, Open by pattern:$this
..... coding:loinc-observation SΣ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: 26436-6
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... coding:observation-category SΣ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
.... text Σ0..1stringPlain text representation of the concept
... code SΣ1..1CodeableConcept​Type of observation (code / type)
Binding: Results Laboratory Observation - IPS (preferred): Intensional Value Set Definition: LOINC { { STATUS in {ACTIVE} CLASSTYPE in {1} CLASS exclude {CHALSKIN, H&P.HX.LAB, H&P.HX, NR STATS, PATH.PROTOCOLS.*} } }

.... id 0..1stringUnique id for inter-element referencing
.... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... Slices for coding SΣ1..*CodingCode defined by a terminology system
Slice: Unordered, Open by pattern:$this
..... coding:loinc SΣ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: 94309-2
...... display1..1stringRepresentation defined by the system
Fixed Value: SARS-CoV-2 (COVID-19) RNA [Presence] in Specimen by NAA with probe detection
...... userSelected0..1booleanIf this coding was chosen directly by the user
...... id 0..1stringUnique id for inter-element referencing
...... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... system SΣ1..1uriIdentity of the terminology system
...... version Σ0..1stringVersion of the system - if relevant
...... code SΣ1..1codeSymbol in syntax defined by the system
...... display Σ0..1stringRepresentation defined by the system
...... userSelected Σ0..1booleanIf this coding was chosen directly by the user
.... text Σ0..1stringPlain text representation of the concept
... subject SΣI1..1Reference(Patient)A reference from one resource to another
... focus ΣI0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter SΣI0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] SΣI1..1dateTimeClinically relevant time/time-period for observation
.... id 0..1stringUnique id for inter-element referencing
.... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... QuelleKlinischesBezugsdatum S0..1CodingOptional Extensions Element
URL: https://www.medizininformatik-initiative.de/fhir/core/modul-labor/StructureDefinition/QuelleKlinischesBezugsdatum
Binding: ValueSetQuelleKlinischesBezugsdatum (required)
.... value 0..1dateTimePrimitive value for dateTime
... issued SΣ0..1instantDate/Time this version was made available
... performer ΣI0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)Who is responsible for the observation
... Slices for value[x] SΣI1..1CodeableConceptActual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept SΣI1..1CodeableConceptActual result
Binding: DetectedNotDetectedInconclusive (required)
..... id 0..1stringUnique id for inter-element referencing
..... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding SΣ1..*CodingCode defined by a terminology system
...... id 0..1stringUnique id for inter-element referencing
...... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... system SΣ1..1uriIdentity of the terminology system
...... version Σ0..1stringVersion of the system - if relevant
...... code SΣ1..1codeSymbol in syntax defined by the system
...... display Σ0..1stringRepresentation defined by the system
...... userSelected Σ0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
... dataAbsentReason SI0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... interpretation S0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


... note S0..*AnnotationComments about the observation
... method S0..1CodeableConceptHow it was done
Binding: ObservationMethods (example): Methods for simple observations.

... specimen SI1..1Reference(Specimen Excreta)Specimen used for this observation
.... id 0..1stringUnique id for inter-element referencing
.... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... reference SΣI0..1stringLiteral reference, Relative, internal or absolute URL
.... type Σ0..1uriType the reference refers to (e.g. "Patient")
Binding: ResourceType (extensible): Aa resource (or, for logical models, the URI of the logical model).

.... identifier SΣ0..1IdentifierLogical reference, when literal reference is not known
.... display Σ0..1stringText alternative for the resource
... device SI0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange SI0..*BackboneElementProvides guide for interpretation
.... id 0..1stringUnique id for inter-element referencing
.... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.

.... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.


.... age I0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember ΣI0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... derivedFrom ΣI0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
... component Σ0..*BackboneElementComponent results
.... id 0..1stringUnique id for inter-element referencing
.... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... value[x] ΣI0..1Actual component result
..... valueQuantityQuantity
..... valueCodeableConceptCodeableConcept
..... valueStringstring
..... valueBooleanboolean
..... valueIntegerinteger
..... valueRangeRange
..... valueRatioRatio
..... valueSampledDataSampledData
..... valueTimetime
..... valueDateTimedateTime
..... valuePeriodPeriod
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

.... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


.... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*ProfileObservationLaboruntersuchungMeasurements and simple assertions
... id Σ0..1stringLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
.... source Σ0..1uriIdentifies where the resource comes from
.... profile Σ0..*canonical(StructureDefinition)Profiles this resource claims to conform to
... Slices for identifier Σ1..*IdentifierBusiness Identifier for observation
Slice: Unordered, Open by pattern:type
.... identifier:analyseBefundCode Σ1..1IdentifierBusiness Identifier for observation
..... type Σ1..1CodeableConceptDescription of identifier
Binding: Identifier Type Codes (extensible): A coded type for an identifier that can be used to determine which identifier to use for a specific purpose.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0203
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: OBI
...... Slices for coding Σ1..*CodingCode defined by a terminology system
Slice: Unordered, Open by value:system
....... coding:observationInstanceV2 Σ1..1CodingCode defined by a terminology system
........ system Σ1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0203
........ code Σ1..1codeSymbol in syntax defined by the system
Fixed Value: OBI
..... system Σ1..1uriThe namespace for the identifier value
..... value Σ1..1stringThe value that is unique
..... assigner ΣI1..1Reference(Organization)A reference from one resource to another
... category 1..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... Slices for coding Σ2..*CodingCode defined by a terminology system
Slice: Unordered, Open by pattern:$this
..... coding:loinc-observation Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: 26436-6
..... coding:observation-category Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
... code Σ1..1CodeableConcept​Type of observation (code / type)
Binding: Results Laboratory Observation - IPS (preferred): Intensional Value Set Definition: LOINC { { STATUS in {ACTIVE} CLASSTYPE in {1} CLASS exclude {CHALSKIN, H&P.HX.LAB, H&P.HX, NR STATS, PATH.PROTOCOLS.*} } }

.... Slices for coding Σ1..*CodingCode defined by a terminology system
Slice: Unordered, Open by pattern:$this
..... coding:loinc Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: 94309-2
...... display1..1stringRepresentation defined by the system
Fixed Value: SARS-CoV-2 (COVID-19) RNA [Presence] in Specimen by NAA with probe detection
...... system Σ1..1uriIdentity of the terminology system
...... code Σ1..1codeSymbol in syntax defined by the system
... subject ΣI1..1Reference(Patient)A reference from one resource to another
... encounter ΣI0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] ΣI1..1dateTimeClinically relevant time/time-period for observation
.... QuelleKlinischesBezugsdatum 0..1CodingOptional Extensions Element
URL: https://www.medizininformatik-initiative.de/fhir/core/modul-labor/StructureDefinition/QuelleKlinischesBezugsdatum
Binding: ValueSetQuelleKlinischesBezugsdatum (required)
... issued Σ0..1instantDate/Time this version was made available
... Slices for value[x] ΣI1..1CodeableConceptActual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣI1..1CodeableConceptActual result
Binding: DetectedNotDetectedInconclusive (required)
..... coding Σ1..*CodingCode defined by a terminology system
...... system Σ1..1uriIdentity of the terminology system
...... code Σ1..1codeSymbol in syntax defined by the system
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


... note 0..*AnnotationComments about the observation
... method 0..1CodeableConceptHow it was done
Binding: ObservationMethods (example): Methods for simple observations.

... specimen I1..1Reference(Specimen Excreta)Specimen used for this observation
.... reference ΣI0..1stringLiteral reference, Relative, internal or absolute URL
.... identifier Σ0..1IdentifierLogical reference, when literal reference is not known
... device I0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation

doco Documentation for this format

​This structure is derived from ProfileObservationLaboruntersuchung

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*ProfileObservationLaboruntersuchungMeasurements and simple assertions
... code
.... Slices for coding S1..*CodingCode defined by a terminology system
Slice: Unordered, Open by pattern:$this
..... coding:loinc S1..1CodingCode defined by a terminology system
Required Pattern: At least the following
...... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: 94309-2
...... display1..1stringRepresentation defined by the system
Fixed Value: SARS-CoV-2 (COVID-19) RNA [Presence] in Specimen by NAA with probe detection
...... system S1..1uriIdentity of the terminology system
...... code S1..1codeSymbol in syntax defined by the system
... subject 1..1Reference(Patient)A reference from one resource to another
... value[x] 1..1CodeableConceptActual result
... valueCodeableConcept 1..1CodeableConceptActual result
Binding: DetectedNotDetectedInconclusive (required)
... specimen 1..1Reference(Specimen Excreta)Specimen used for this observation

doco Documentation for this format

​This structure is derived from ProfileObservationLaboruntersuchung

Summary

Mandatory: 7 elements
Must-Support: 4 elements
Prohibited: 1 element

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element Observation.code.coding is sliced based on the value of pattern:$this

 

Other representations of profile: CSV, Excel, Schematron

Terminology Bindings

PathConformanceValueSet / Code
Observation.meta.securityextensibleAll Security Labels
Observation.meta.tagexampleCommonTags
Observation.languagepreferredCommonLanguages
Max Binding: AllLanguages
Observation.identifier:analyseBefundCode.userequiredIdentifierUse
Observation.identifier:analyseBefundCode.typeextensiblePattern: OBI
Observation.statusrequiredObservationStatus
Observation.categorypreferredObservationCategoryCodes
Observation.codepreferred​ResultsLabObservationUvIps
Observation.value[x]:valueQuantity.comparatorrequiredQuantityComparator
Observation.value[x]:valueCodeableConceptrequired​DetectedNotDetectedInconclusive (missing link)
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.interpretationextensibleObservationInterpretationCodes
Observation.methodexampleObservationMethods
Observation.specimen.typeextensibleResourceType
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
Observation.component.codeexampleLOINCCodes
Observation.component.dataAbsentReasonextensibleDataAbsentReason
Observation.component.interpretationextensibleObservationInterpretationCodes