NCPI FHIR Implementation Guide
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Resource Profile: Raw Data Observation

Official URL: https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/raw-data-observation Version: 0.1.0
Active as of 2022-08-17 Computable Name: RawDataObservation

Representation for a row of data from one of the dataset’s tables.

Code Must be Present

While there may be more than one coding associated with these Observations, one of them must be the code from the Table’s data-dictionary entry in the data-set CodeSystem. This provides basic context associated with what the contents of the resource relate to.

Components Represent the Row’s Columns

Each of these Observations represents a single row from a single table from the study’s dataset. The individual cells are captured as components such that each non-missing data point will be stored in a separate component.

There must be at least one component present.

Usage:

  • This Resource Profile is not used by any profiles in this Implementation Guide

Formal Views of Profile Content

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

This structure is derived from Observation

Summary

Mandatory: 2 elements

This structure is derived from Observation

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*ObservationMeasurements and simple assertions
... code
.... coding 1..*CodingCode defined by a terminology system
... component 1..*BackboneElementComponent results

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*ObservationMeasurements 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
... identifier Σ0..*IdentifierBusiness Identifier for observation
... 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 ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... category 0..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


... code Σ1..1CodeableConceptType of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... coding Σ1..*CodingCode defined by a terminology system
.... text Σ0..1stringPlain text representation of the concept
... subject Σ0..1Reference(Patient | Group | Device | Location)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] Σ0..1Clinically relevant time/time-period for observation
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
.... effectiveTimingTiming
.... effectiveInstantinstant
... issued Σ0..1instantDate/Time this version was made available
... performer Σ0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)Who is responsible for the observation
... value[x] ΣI0..1Actual result
.... valueQuantityQuantity
.... valueCodeableConceptCodeableConcept
.... valueStringstring
.... valueBooleanboolean
.... valueIntegerinteger
.... valueRangeRange
.... valueRatioRatio
.... valueSampledDataSampledData
.... valueTimetime
.... valueDateTimedateTime
.... valuePeriodPeriod
... 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
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

... 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
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
... component Σ1..*BackboneElementComponent results
.... 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
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... value[x] Σ0..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

This structure is derived from Observation

Summary

Mandatory: 2 elements

Differential View

This structure is derived from Observation

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*ObservationMeasurements and simple assertions
... code
.... coding 1..*CodingCode defined by a terminology system
... component 1..*BackboneElementComponent results

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*ObservationMeasurements 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
... identifier Σ0..*IdentifierBusiness Identifier for observation
... 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 ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... category 0..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


... code Σ1..1CodeableConceptType of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... coding Σ1..*CodingCode defined by a terminology system
.... text Σ0..1stringPlain text representation of the concept
... subject Σ0..1Reference(Patient | Group | Device | Location)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] Σ0..1Clinically relevant time/time-period for observation
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
.... effectiveTimingTiming
.... effectiveInstantinstant
... issued Σ0..1instantDate/Time this version was made available
... performer Σ0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)Who is responsible for the observation
... value[x] ΣI0..1Actual result
.... valueQuantityQuantity
.... valueCodeableConceptCodeableConcept
.... valueStringstring
.... valueBooleanboolean
.... valueIntegerinteger
.... valueRangeRange
.... valueRatioRatio
.... valueSampledDataSampledData
.... valueTimetime
.... valueDateTimedateTime
.... valuePeriodPeriod
... 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
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

... 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
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
... component Σ1..*BackboneElementComponent results
.... 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
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... value[x] Σ0..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

 

Other representations of profile: CSV, Excel, Schematron

Terminology Bindings

PathConformanceValueSet
Observation.languagepreferredCommonLanguages
Max Binding: AllLanguages
Observation.statusrequiredObservationStatus
Observation.categorypreferredObservationCategoryCodes
Observation.codeexampleLOINCCodes
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.interpretationextensibleObservationInterpretationCodes
Observation.bodySiteexampleSNOMEDCTBodyStructures
Observation.methodexampleObservationMethods
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
Observation.component.codeexampleLOINCCodes
Observation.component.dataAbsentReasonextensibleDataAbsentReason
Observation.component.interpretationextensibleObservationInterpretationCodes

Constraints

IdGradePathDetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource
: contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4errorObservationIf a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
: contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6Best PracticeObservationA resource should have narrative for robust management
: text.`div`.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
: value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
ele-1errorObservation.metaAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.implicitRulesAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.languageAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.textAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.identifierAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.basedOnAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.partOfAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.statusAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.categoryAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.code.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.code.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.code.codingAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.code.textAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.subjectAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.focusAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.encounterAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.effective[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.issuedAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.performerAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.interpretationAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.noteAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.bodySiteAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.methodAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.specimenAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.deviceAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
obs-3errorObservation.referenceRangeMust have at least a low or a high or text
: low.exists() or high.exists() or text.exists()
ele-1errorObservation.referenceRange.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.referenceRange.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.referenceRange.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.referenceRange.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.referenceRange.lowAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.referenceRange.highAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.referenceRange.typeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.referenceRange.appliesToAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.referenceRange.ageAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.referenceRange.textAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.hasMemberAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.derivedFromAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component.interpretationAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())

Notes:

Component Definition

The components represent non-missing data from the table of origin for the given row. As such, each will have some data stored in the value[x] property, along with a proper code from the table’s data-dictionary CodeSystem.

Data Dictionary Codes Provide Context

In order to establish what each of the components represents, one of the component’s codings should point to the appropriate code from the related table’s data-dictionary CodeSystem.

Typed Data is Encouraged Within Limits

Given a reasonably complete data-dictionary, it should be possible to properly type most of the data and correctly assign those typed data to the appropriate value[x] properties. Where the data actually fails to conform to the data-dictionary’s established type, the resource will validate fine with an appropriate value[x] type that can support the non-conforming data, such as signifying NaN as a code for non-numeric numerics, or choosing a valueString to handle cases like “< 1”.

In general, it is assumed decimal numbers will be represented as valueQuantity, however, unless there is some specification from the data-dictionary about the value’s type, that quantity may simply contain the singular value property.

Each Non-Missing Column Should be Present

While it may seem appropriate to merge certain types of columns together to take advantage of their known relationship, such as using a separate column’s contents to assign the units associated with a quantity, the objective here is to establish as accurate a picture of what the original data looked like as possible. As such, resource generators should avoid any such transformations for these raw data resources. Leave those to the interoperable portion of the FHIR transformation.