COVID-19 FHIR Profile Library IG Informative Version
1.0.0 - Informative US

This page is part of the Logica COVID-19 FHIR Profile Library IG (v1.0.0: Informative - Informative) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions

Resource Profile: SARS-CoV-2 (COVID-19) sequencing and identification panel - Specimen by Molecular genetics method

Official URL: http://hl7.org/fhir/us/covid19library/StructureDefinition/SARScoronavirus2sequencingidentificationpanelPtXXXMolgen Version: 1.0.0
Active as of 2022-07-25 Computable Name: SARScoronavirus2sequencingidentificationpanelPtXXXMolgen

Copyright/Legal: HL7 International & Logica Health, all rights reserved Creative Commons License

A collection of laboratory tests for the detection of SARS-CoV-2 in unspecified specimen via sequencing

Usage:

Formal Views of Profile Content

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

This structure is derived from LaboratoryObservationPanelBase

Summary

Structures

This structure refers to these other structures:

This structure is derived from LaboratoryObservationPanelBase

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*LaboratoryObservationPanelBaseMeasurements and simple assertions
... code 1..1CodeableConceptLaboratory Test Name
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://loinc.org
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 96894-1
... hasMember:SequencingStudyIdentifier 0..1Reference(Sequencing Study Identifier)Related resource that belongs to the Observation group
... hasMember:GISAIDSequenceAccessionNumber 0..1Reference(GISAID Sequence Accession Number)Related resource that belongs to the Observation group
... hasMember:SARScoronavirus2SgenemutationdetectedPridPtXXXNomMolgen 0..1Reference(SARS-CoV-2 (COVID-19) S gene mutation detected [Identifier] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
... hasMember:SARScoronavirus2SgenemutationPrThrPtXXXOrdMolgen 0..1Reference(SARS-CoV-2 (COVID-19) S gene mutation [Presence] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
... hasMember:SARScoronavirus2cladeTypePtXXXNomMolgen 0..1Reference(SARS-CoV-2 (COVID-19) clade [Type] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
... hasMember:SARScoronavirus2lineagePridPtXXXNomMolgen 0..1Reference(SARS-CoV-2 (COVID-19) lineage [Identifier] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
... hasMember:SARScoronavirus2variantTypePtXXXNomSequencing 0..1Reference(SARS-CoV-2 (COVID-19) variant [Type] in Specimen by Sequencing)Related resource that belongs to the Observation group
... hasMember:SARScoronavirus2variantinterpretationImpPtXXXNar 0..1Reference(SARS-CoV-2 (COVID-19) variant interpretation in Specimen Narrative)Related resource that belongs to the Observation group

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*LaboratoryObservationPanelBaseMeasurements and simple assertions
... id Σ0..1stringLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguagesMax Binding
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... Slices for identifier Σ0..*IdentifierBusiness Identifier for observation
Slice: Unordered, Open by pattern:type
.... identifier:accessionIdentifier Σ0..1IdentifierBusiness Identifier for observation
..... id 0..1stringUnique id for inter-element referencing
..... 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 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
...... 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: ACSN
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... system Σ0..1uriThe namespace for the identifier value
Example General: http://www.acme.com/identifiers/patient
..... value Σ0..1stringThe value that is unique
Example General: 123456
..... period Σ0..1PeriodTime period when id is/was valid for use
..... assigner Σ0..1Reference(Organization)Organization that issued id (may be just text)
.... identifier:fillerOrderNumber Σ0..1IdentifierBusiness Identifier for observation
..... id 0..1stringUnique id for inter-element referencing
..... 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 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
...... 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: FILL
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... system Σ0..1uriThe namespace for the identifier value
Example General: http://www.acme.com/identifiers/patient
..... value Σ0..1stringThe value that is unique
Example General: 123456
..... period Σ0..1PeriodTime period when id is/was valid for use
..... assigner Σ0..1Reference(Organization)Organization that issued id (may be just text)
.... identifier:placerOrderNumber Σ0..1IdentifierBusiness Identifier for observation
..... id 0..1stringUnique id for inter-element referencing
..... 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 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
...... 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: PLAC
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... system Σ0..1uriThe namespace for the identifier value
Example General: http://www.acme.com/identifiers/patient
..... value Σ0..1stringThe value that is unique
Example General: 123456
..... period Σ0..1PeriodTime period when id is/was valid for use
..... assigner Σ0..1Reference(Organization)Organization that issued id (may be just text)
... basedOn Σ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... Slices for category S1..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by pattern:$this
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:Laboratory S1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



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/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
..... text0..1stringPlain text representation of the concept
... code SΣ1..1CodeableConceptLaboratory Test Name
Binding: LOINCCodes (extensible): LOINC codes


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://loinc.org
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 96894-1
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... subject SΣ1..1Reference(US Core Patient Profile)Who and/or what the observation is about
... focus Σ0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] SΣI0..1Clinically relevant time/time-period for observation
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
... issued Σ0..1instantDate/Time this version was made available
... Slices for performer Σ0..*Reference(Practitioner | Organization)Who is responsible for the observation
Slice: Unordered, Open by value:Observation.performer
.... performer:responsibleObserver Σ0..1Reference(Practitioner)Who is responsible for the observation
.... performer:performingLaboratory Σ0..1Reference(Organization)Who is responsible for the observation
.... performer:performingOrganizationMedicalDirector Σ0..1Reference(Practitioner)Who is responsible for the observation
... dataAbsentReason SI0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)
... 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 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... 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 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... Slices for hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
Slice: Unordered, Open by profile:$this.resolve()
.... hasMember:SequencingStudyIdentifier Σ0..1Reference(Sequencing Study Identifier)Related resource that belongs to the Observation group
.... hasMember:GISAIDSequenceAccessionNumber Σ0..1Reference(GISAID Sequence Accession Number)Related resource that belongs to the Observation group
.... hasMember:SARSCoV2wholegenomeSeqPtIsolateNomSequencing Σ0..1Reference(SARS-coV-2 (COVID19) whole genome [Nucleiotide sequence] in Isolate by Sequencing)Related resource that belongs to the Observation group
.... hasMember:SARScoronavirus2SgenemutationdetectedPridPtXXXNomMolgen Σ0..1Reference(SARS-CoV-2 (COVID-19) S gene mutation detected [Identifier] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
.... hasMember:SARScoronavirus2SgenemutationPrThrPtXXXOrdMolgen Σ0..1Reference(SARS-CoV-2 (COVID-19) S gene mutation [Presence] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
.... hasMember:SARScoronavirus2cladeTypePtXXXNomMolgen Σ0..1Reference(SARS-CoV-2 (COVID-19) clade [Type] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
.... hasMember:SARScoronavirus2lineagePridPtXXXNomMolgen Σ0..1Reference(SARS-CoV-2 (COVID-19) lineage [Identifier] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
.... hasMember:SARScoronavirus2variantTypePtXXXNomSequencing Σ0..1Reference(SARS-CoV-2 (COVID-19) variant [Type] in Specimen by Sequencing)Related resource that belongs to the Observation group
.... hasMember:SARScoronavirus2variantinterpretationImpPtXXXNar Σ0..1Reference(SARS-CoV-2 (COVID-19) variant interpretation in Specimen Narrative)Related resource that belongs to the Observation group
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*LaboratoryObservationPanelBaseMeasurements and simple assertions
... status ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... Slices for category 1..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by pattern:$this
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:Laboratory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



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/observation-category
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
... code Σ1..1CodeableConceptLaboratory Test Name
Binding: LOINCCodes (extensible): LOINC codes


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://loinc.org
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 96894-1
... effective[x] ΣI0..1Clinically relevant time/time-period for observation
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)

doco Documentation for this format

This structure is derived from LaboratoryObservationPanelBase

Summary

Structures

This structure refers to these other structures:

Differential View

This structure is derived from LaboratoryObservationPanelBase

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*LaboratoryObservationPanelBaseMeasurements and simple assertions
... code 1..1CodeableConceptLaboratory Test Name
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://loinc.org
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 96894-1
... hasMember:SequencingStudyIdentifier 0..1Reference(Sequencing Study Identifier)Related resource that belongs to the Observation group
... hasMember:GISAIDSequenceAccessionNumber 0..1Reference(GISAID Sequence Accession Number)Related resource that belongs to the Observation group
... hasMember:SARScoronavirus2SgenemutationdetectedPridPtXXXNomMolgen 0..1Reference(SARS-CoV-2 (COVID-19) S gene mutation detected [Identifier] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
... hasMember:SARScoronavirus2SgenemutationPrThrPtXXXOrdMolgen 0..1Reference(SARS-CoV-2 (COVID-19) S gene mutation [Presence] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
... hasMember:SARScoronavirus2cladeTypePtXXXNomMolgen 0..1Reference(SARS-CoV-2 (COVID-19) clade [Type] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
... hasMember:SARScoronavirus2lineagePridPtXXXNomMolgen 0..1Reference(SARS-CoV-2 (COVID-19) lineage [Identifier] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
... hasMember:SARScoronavirus2variantTypePtXXXNomSequencing 0..1Reference(SARS-CoV-2 (COVID-19) variant [Type] in Specimen by Sequencing)Related resource that belongs to the Observation group
... hasMember:SARScoronavirus2variantinterpretationImpPtXXXNar 0..1Reference(SARS-CoV-2 (COVID-19) variant interpretation in Specimen Narrative)Related resource that belongs to the Observation group

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*LaboratoryObservationPanelBaseMeasurements and simple assertions
... id Σ0..1stringLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguagesMax Binding
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... Slices for identifier Σ0..*IdentifierBusiness Identifier for observation
Slice: Unordered, Open by pattern:type
.... identifier:accessionIdentifier Σ0..1IdentifierBusiness Identifier for observation
..... id 0..1stringUnique id for inter-element referencing
..... 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 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
...... 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: ACSN
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... system Σ0..1uriThe namespace for the identifier value
Example General: http://www.acme.com/identifiers/patient
..... value Σ0..1stringThe value that is unique
Example General: 123456
..... period Σ0..1PeriodTime period when id is/was valid for use
..... assigner Σ0..1Reference(Organization)Organization that issued id (may be just text)
.... identifier:fillerOrderNumber Σ0..1IdentifierBusiness Identifier for observation
..... id 0..1stringUnique id for inter-element referencing
..... 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 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
...... 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: FILL
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... system Σ0..1uriThe namespace for the identifier value
Example General: http://www.acme.com/identifiers/patient
..... value Σ0..1stringThe value that is unique
Example General: 123456
..... period Σ0..1PeriodTime period when id is/was valid for use
..... assigner Σ0..1Reference(Organization)Organization that issued id (may be just text)
.... identifier:placerOrderNumber Σ0..1IdentifierBusiness Identifier for observation
..... id 0..1stringUnique id for inter-element referencing
..... 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 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
...... 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: PLAC
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... system Σ0..1uriThe namespace for the identifier value
Example General: http://www.acme.com/identifiers/patient
..... value Σ0..1stringThe value that is unique
Example General: 123456
..... period Σ0..1PeriodTime period when id is/was valid for use
..... assigner Σ0..1Reference(Organization)Organization that issued id (may be just text)
... basedOn Σ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... Slices for category S1..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by pattern:$this
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:Laboratory S1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



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/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
..... text0..1stringPlain text representation of the concept
... code SΣ1..1CodeableConceptLaboratory Test Name
Binding: LOINCCodes (extensible): LOINC codes


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://loinc.org
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 96894-1
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... subject SΣ1..1Reference(US Core Patient Profile)Who and/or what the observation is about
... focus Σ0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] SΣI0..1Clinically relevant time/time-period for observation
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
... issued Σ0..1instantDate/Time this version was made available
... Slices for performer Σ0..*Reference(Practitioner | Organization)Who is responsible for the observation
Slice: Unordered, Open by value:Observation.performer
.... performer:responsibleObserver Σ0..1Reference(Practitioner)Who is responsible for the observation
.... performer:performingLaboratory Σ0..1Reference(Organization)Who is responsible for the observation
.... performer:performingOrganizationMedicalDirector Σ0..1Reference(Practitioner)Who is responsible for the observation
... dataAbsentReason SI0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)
... 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 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... 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 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... Slices for hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
Slice: Unordered, Open by profile:$this.resolve()
.... hasMember:SequencingStudyIdentifier Σ0..1Reference(Sequencing Study Identifier)Related resource that belongs to the Observation group
.... hasMember:GISAIDSequenceAccessionNumber Σ0..1Reference(GISAID Sequence Accession Number)Related resource that belongs to the Observation group
.... hasMember:SARSCoV2wholegenomeSeqPtIsolateNomSequencing Σ0..1Reference(SARS-coV-2 (COVID19) whole genome [Nucleiotide sequence] in Isolate by Sequencing)Related resource that belongs to the Observation group
.... hasMember:SARScoronavirus2SgenemutationdetectedPridPtXXXNomMolgen Σ0..1Reference(SARS-CoV-2 (COVID-19) S gene mutation detected [Identifier] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
.... hasMember:SARScoronavirus2SgenemutationPrThrPtXXXOrdMolgen Σ0..1Reference(SARS-CoV-2 (COVID-19) S gene mutation [Presence] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
.... hasMember:SARScoronavirus2cladeTypePtXXXNomMolgen Σ0..1Reference(SARS-CoV-2 (COVID-19) clade [Type] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
.... hasMember:SARScoronavirus2lineagePridPtXXXNomMolgen Σ0..1Reference(SARS-CoV-2 (COVID-19) lineage [Identifier] in Specimen by Molecular genetics method)Related resource that belongs to the Observation group
.... hasMember:SARScoronavirus2variantTypePtXXXNomSequencing Σ0..1Reference(SARS-CoV-2 (COVID-19) variant [Type] in Specimen by Sequencing)Related resource that belongs to the Observation group
.... hasMember:SARScoronavirus2variantinterpretationImpPtXXXNar Σ0..1Reference(SARS-CoV-2 (COVID-19) variant interpretation in Specimen Narrative)Related resource that belongs to the Observation group
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from

doco Documentation for this format

 

Other representations of profile: CSV, Excel, Schematron

Terminology Bindings

PathConformanceValueSet / Code
Observation.languagepreferredCommonLanguages
Max Binding: AllLanguages
Observation.identifier:accessionIdentifier.userequiredIdentifierUse
Observation.identifier:accessionIdentifier.typeextensiblePattern: ACSN
Observation.identifier:fillerOrderNumber.userequiredIdentifierUse
Observation.identifier:fillerOrderNumber.typeextensiblePattern: FILL
Observation.identifier:placerOrderNumber.userequiredIdentifierUse
Observation.identifier:placerOrderNumber.typeextensiblePattern: PLAC
Observation.statusrequiredObservationStatus
Observation.categorypreferredObservationCategoryCodes
Observation.category:LaboratorypreferredPattern: laboratory
Observation.codeextensiblePattern: LOINC code 96894-1
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.interpretationextensibleObservationInterpretationCodes
Observation.methodexampleObservationMethods
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
Observation.component.codeexampleLOINCCodes
Observation.component.dataAbsentReasonextensibleDataAbsentReason
Observation.component.interpretationextensibleObservationInterpretationCodes