NCPI FHIR Implementation Guide v2 - Local Development build (v0.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

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Resource Profile: NCPI FASTQ File

NCPI FASTQ File

Usage:

• Examples for this Resource Profile: Observation/FASTQ-example

Formal Views of Profile Content

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

• Differential Table
• Key Elements Table
• Snapshot Table
• Statistics/References
• All

This structure is derived from NcpiFileMetadata

Name	Flags	Card.	Type	Description & Constraints
Observation		0..*	NcpiFileMetadata	Measurements and simple assertions
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
specimen-collection		0..*	Reference()	Linkage for related samples URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection
Slices for component		7..*	BackboneElement	Component results Slice: Unordered, Open by value:code
component:assay_strategy		1..1	BackboneElement	Component results
code		1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: AssayStrategy
value[x]		0..1	CodeableConcept	Actual component result
component:platform_instrument		1..1	BackboneElement	Component results
code		1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: PlatformInstrument
value[x]		0..1	CodeableConcept	Actual component result
component:library_prep		1..1	BackboneElement	Component results
code		1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: LibraryPrep
value[x]		0..1	CodeableConcept	Actual component result
component:library_selection		1..1	BackboneElement	Component results
code		1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: LibrarySelection
value[x]		0..1	CodeableConcept	Actual component result
component:strandedness		1..1	BackboneElement	Component results
code		1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: Strandedness
value[x]		0..1	CodeableConcept	Actual component result
component:target_region		0..1	BackboneElement	Component results
code		1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: TargetRegion
value[x]		0..1	CodeableConcept	Actual component result
component:is_paired_end		1..1	BackboneElement	Component results
code		1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: IsPairedEnd
value[x]		0..1		Actual component result
valueCodeableConcept			CodeableConcept
valueBoolean			boolean
component:adaptor_trimmed		1..1	BackboneElement	Component results
code		1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: AdaptorTrimmed
value[x]		0..1		Actual component result
valueCodeableConcept			CodeableConcept
valueBoolean			boolean
component:reference_genome		0..1	BackboneElement	Component results
code		1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: ReferenceGenome
value[x]		0..1	CodeableConcept	Actual component result
component:workflow_type		0..1	BackboneElement	Component results
code		1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: WorkflowType
value[x]		0..1	CodeableConcept	Actual component result
component:workflow_tool		0..1	BackboneElement	Component results
code		1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: WorkflowTool
value[x]		0..1	CodeableConcept	Actual component result
Documentation for this format

Name	Flags	Card.	Type	Description & Constraints
Observation	C	0..*	NcpiFileMetadata	Measurements and simple assertions obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
specimen-collection		0..*	Reference()	Linkage for related samples URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
status	?!Σ	1..1	code	registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation.
code	Σ	1..1	CodeableConcept	Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
focus	Σ	1..1	Reference(Resource)	What the observation is about, when it is not about the subject of record
Slices for component	Σ	7..*	BackboneElement	Component results Slice: Unordered, Open by value:code
component:All Slices				Content/Rules for all slices
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
component:assay_strategy	Σ	1..1	BackboneElement	Component results
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: AssayStrategy
value[x]	Σ	0..1	CodeableConcept	Actual component result
component:platform_instrument	Σ	1..1	BackboneElement	Component results
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: PlatformInstrument
value[x]	Σ	0..1	CodeableConcept	Actual component result
component:library_prep	Σ	1..1	BackboneElement	Component results
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: LibraryPrep
value[x]	Σ	0..1	CodeableConcept	Actual component result
component:library_selection	Σ	1..1	BackboneElement	Component results
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: LibrarySelection
value[x]	Σ	0..1	CodeableConcept	Actual component result
component:strandedness	Σ	1..1	BackboneElement	Component results
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: Strandedness
value[x]	Σ	0..1	CodeableConcept	Actual component result
component:target_region	Σ	0..1	BackboneElement	Component results
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: TargetRegion
value[x]	Σ	0..1	CodeableConcept	Actual component result
component:is_paired_end	Σ	1..1	BackboneElement	Component results
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: IsPairedEnd
value[x]	Σ	0..1		Actual component result
valueCodeableConcept			CodeableConcept
valueBoolean			boolean
component:adaptor_trimmed	Σ	1..1	BackboneElement	Component results
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: AdaptorTrimmed
value[x]	Σ	0..1		Actual component result
valueCodeableConcept			CodeableConcept
valueBoolean			boolean
component:reference_genome	Σ	0..1	BackboneElement	Component results
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: ReferenceGenome
value[x]	Σ	0..1	CodeableConcept	Actual component result
component:workflow_type	Σ	0..1	BackboneElement	Component results
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: WorkflowType
value[x]	Σ	0..1	CodeableConcept	Actual component result
component:workflow_tool	Σ	0..1	BackboneElement	Component results
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
code		1..1	code	Symbol in syntax defined by the system Fixed Value: WorkflowTool
value[x]	Σ	0..1	CodeableConcept	Actual component result
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet / Code	URI
Observation.status	required	ObservationStatus http://hl7.org/fhir/ValueSet/observation-status|4.3.0 from the FHIR Standard
Observation.code	example	LOINCCodes (a valid code from LOINC) http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component.code	example	LOINCCodes (a valid code from LOINC) http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:assay_strategy.code	example	Pattern: AssayStrategy http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:platform_instrument.code	example	Pattern: PlatformInstrument http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:library_prep.code	example	Pattern: LibraryPrep http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:library_selection.code	example	Pattern: LibrarySelection http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:strandedness.code	example	Pattern: Strandedness http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:target_region.code	example	Pattern: TargetRegion http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:is_paired_end.code	example	Pattern: IsPairedEnd http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:adaptor_trimmed.code	example	Pattern: AdaptorTrimmed http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:reference_genome.code	example	Pattern: ReferenceGenome http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:workflow_type.code	example	Pattern: WorkflowType http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:workflow_tool.code	example	Pattern: WorkflowTool http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Constraints Id Grade Path(s) Details Requirements dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where(((id.exists() and ('#'+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(uri) = '#').exists()).not()).trace('unmatched', id).empty() dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() dom-6 best practice Observation A resource should have narrative for robust management : text.`div`.exists() ele-1 error **ALL** elements All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) ext-1 error **ALL** extensions Must have either extensions or value[x], not both : extension.exists() != value.exists() obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() obs-7 error Observation If 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() Name Flags Card. Type Description & Constraints Observation C 0..* NcpiFileMetadata Measurements and simple assertions obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present id Σ 0..1 id Logical id of this artifact meta Σ 0..1 Meta Metadata about the resource implicitRules ?!Σ 0..1 uri A set of rules under which this content was created language 0..1 code Language of the resource content Binding: CommonLanguages (preferred): IETF language tag Additional Bindings Purpose AllLanguages Max Binding text 0..1 Narrative Text summary of the resource, for human interpretation contained 0..* Resource Contained, inline Resources dom-r4b: Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url specimen-collection 0..* Reference() Linkage for related samples URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection modifierExtension ?! 0..* Extension Extensions that cannot be ignored identifier Σ 0..* Identifier Business Identifier for observation basedOn Σ 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) Part of referenced event status ?!Σ 1..1 code registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. category 0..* CodeableConcept Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. code Σ 1..1 CodeableConcept Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. subject Σ 0..1 Reference(Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance) Who and/or what the observation is about focus Σ 1..1 Reference(Resource) What the observation is about, when it is not about the subject of record encounter Σ 0..1 Reference(Encounter) Healthcare event during which this observation is made effective[x] Σ 0..1 Clinically relevant time/time-period for observation effectiveDateTime dateTime effectivePeriod Period effectiveTiming Timing effectiveInstant instant issued Σ 0..1 instant Date/Time this version was made available performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Who is responsible for the observation value[x] ΣC 0..1 Actual result valueQuantity Quantity valueCodeableConcept CodeableConcept valueString string valueBoolean boolean valueInteger integer valueRange Range valueRatio Ratio valueSampledData SampledData valueTime time valueDateTime dateTime valuePeriod Period dataAbsentReason C 0..1 CodeableConcept Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. note 0..* Annotation Comments about the observation bodySite 0..1 CodeableConcept Observed body part Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts method 0..1 CodeableConcept How it was done Binding: ObservationMethods (example): Methods for simple observations. specimen 0..1 Reference(Specimen) Specimen used for this observation device 0..1 Reference(Device | DeviceMetric) (Measurement) Device referenceRange C 0..* BackboneElement Provides guide for interpretation obs-3: Must have at least a low or a high or text id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized low C 0..1 SimpleQuantity Low Range, if relevant high C 0..1 SimpleQuantity High Range, if relevant type 0..1 CodeableConcept Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range. appliesTo 0..* CodeableConcept Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to. age 0..1 Range Applicable age range, if relevant text 0..1 string Text based reference range in an observation hasMember Σ 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Related resource that belongs to the Observation group derivedFrom Σ 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from Slices for component Σ 7..* BackboneElement Component results Slice: Unordered, Open by value:code component:All Slices Content/Rules for all slices id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. value[x] Σ 0..1 Actual component result valueQuantity Quantity valueCodeableConcept CodeableConcept valueString string valueBoolean boolean valueInteger integer valueRange Range valueRatio Ratio valueSampledData SampledData valueTime time valueDateTime dateTime valuePeriod Period dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:assay_strategy Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: AssayStrategy display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:platform_instrument Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: PlatformInstrument display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:library_prep Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: LibraryPrep display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:library_selection Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: LibrarySelection display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:strandedness Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: Strandedness display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:target_region Σ 0..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: TargetRegion display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:is_paired_end Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: IsPairedEnd display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 Actual component result valueCodeableConcept CodeableConcept valueBoolean boolean dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:adaptor_trimmed Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: AdaptorTrimmed display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 Actual component result valueCodeableConcept CodeableConcept valueBoolean boolean dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:reference_genome Σ 0..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: ReferenceGenome display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:workflow_type Σ 0..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: WorkflowType display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:workflow_tool Σ 0..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: WorkflowTool display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result Documentation for this format Terminology Bindings Constraints Path Conformance ValueSet / Code URI Observation.language preferred CommonLanguages Additional Bindings Purpose AllLanguages Max Binding http://hl7.org/fhir/ValueSet/languages from the FHIR Standard Observation.status required ObservationStatus http://hl7.org/fhir/ValueSet/observation-status|4.3.0 from the FHIR Standard Observation.category preferred ObservationCategoryCodes http://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard Observation.code example LOINCCodes (a valid code from LOINC) http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.bodySite example SNOMEDCTBodyStructures http://hl7.org/fhir/ValueSet/body-site from the FHIR Standard Observation.method example ObservationMethods http://hl7.org/fhir/ValueSet/observation-methods from the FHIR Standard Observation.referenceRange.type preferred ObservationReferenceRangeMeaningCodes http://hl7.org/fhir/ValueSet/referencerange-meaning from the FHIR Standard Observation.referenceRange.appliesTo example ObservationReferenceRangeAppliesToCodes http://hl7.org/fhir/ValueSet/referencerange-appliesto from the FHIR Standard Observation.component.code example LOINCCodes (a valid code from LOINC) http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:assay_strategy.code example Pattern: AssayStrategy http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:assay_strategy.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:assay_strategy.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:platform_instrument.code example Pattern: PlatformInstrument http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:platform_instrument.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:platform_instrument.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:library_prep.code example Pattern: LibraryPrep http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:library_prep.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:library_prep.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:library_selection.code example Pattern: LibrarySelection http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:library_selection.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:library_selection.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:strandedness.code example Pattern: Strandedness http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:strandedness.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:strandedness.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:target_region.code example Pattern: TargetRegion http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:target_region.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:target_region.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:is_paired_end.code example Pattern: IsPairedEnd http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:is_paired_end.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:is_paired_end.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:adaptor_trimmed.code example Pattern: AdaptorTrimmed http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:adaptor_trimmed.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:adaptor_trimmed.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:reference_genome.code example Pattern: ReferenceGenome http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:reference_genome.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:reference_genome.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:workflow_type.code example Pattern: WorkflowType http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:workflow_type.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:workflow_type.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:workflow_tool.code example Pattern: WorkflowTool http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:workflow_tool.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:workflow_tool.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Id Grade Path(s) Details Requirements dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where(((id.exists() and ('#'+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(uri) = '#').exists()).not()).trace('unmatched', id).empty() dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() dom-6 best practice Observation A resource should have narrative for robust management : text.`div`.exists() dom-r4b warning Observation.contained Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems : ($this is Citation or $this is Evidence or $this is EvidenceReport or $this is EvidenceVariable or $this is MedicinalProductDefinition or $this is PackagedProductDefinition or $this is AdministrableProductDefinition or $this is Ingredient or $this is ClinicalUseDefinition or $this is RegulatedAuthorization or $this is SubstanceDefinition or $this is SubscriptionStatus or $this is SubscriptionTopic) implies (%resource is Citation or %resource is Evidence or %resource is EvidenceReport or %resource is EvidenceVariable or %resource is MedicinalProductDefinition or %resource is PackagedProductDefinition or %resource is AdministrableProductDefinition or %resource is Ingredient or %resource is ClinicalUseDefinition or %resource is RegulatedAuthorization or %resource is SubstanceDefinition or %resource is SubscriptionStatus or %resource is SubscriptionTopic) ele-1 error **ALL** elements All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) ext-1 error **ALL** extensions Must have either extensions or value[x], not both : extension.exists() != value.exists() obs-3 error Observation.referenceRange Must have at least a low or a high or text : low.exists() or high.exists() or text.exists() obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() obs-7 error Observation If 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() This structure is derived from NcpiFileMetadata Summary Mandatory: 7 elements Extensions This structure refers to these extensions: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection Slices This structure defines the following Slices: The element 1 is sliced based on the value of Observation.component Differential View This structure is derived from NcpiFileMetadata Name Flags Card. Type Description & Constraints Observation 0..* NcpiFileMetadata Measurements and simple assertions Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url specimen-collection 0..* Reference() Linkage for related samples URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection Slices for component 7..* BackboneElement Component results Slice: Unordered, Open by value:code component:assay_strategy 1..1 BackboneElement Component results code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: AssayStrategy value[x] 0..1 CodeableConcept Actual component result component:platform_instrument 1..1 BackboneElement Component results code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: PlatformInstrument value[x] 0..1 CodeableConcept Actual component result component:library_prep 1..1 BackboneElement Component results code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: LibraryPrep value[x] 0..1 CodeableConcept Actual component result component:library_selection 1..1 BackboneElement Component results code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: LibrarySelection value[x] 0..1 CodeableConcept Actual component result component:strandedness 1..1 BackboneElement Component results code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: Strandedness value[x] 0..1 CodeableConcept Actual component result component:target_region 0..1 BackboneElement Component results code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: TargetRegion value[x] 0..1 CodeableConcept Actual component result component:is_paired_end 1..1 BackboneElement Component results code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: IsPairedEnd value[x] 0..1 Actual component result valueCodeableConcept CodeableConcept valueBoolean boolean component:adaptor_trimmed 1..1 BackboneElement Component results code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: AdaptorTrimmed value[x] 0..1 Actual component result valueCodeableConcept CodeableConcept valueBoolean boolean component:reference_genome 0..1 BackboneElement Component results code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: ReferenceGenome value[x] 0..1 CodeableConcept Actual component result component:workflow_type 0..1 BackboneElement Component results code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: WorkflowType value[x] 0..1 CodeableConcept Actual component result component:workflow_tool 0..1 BackboneElement Component results code 1..1 CodeableConcept Type of component observation (code / type) Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: WorkflowTool value[x] 0..1 CodeableConcept Actual component result Documentation for this format Key Elements View Name Flags Card. Type Description & Constraints Observation C 0..* NcpiFileMetadata Measurements and simple assertions obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present implicitRules ?!Σ 0..1 uri A set of rules under which this content was created Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url specimen-collection 0..* Reference() Linkage for related samples URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection modifierExtension ?! 0..* Extension Extensions that cannot be ignored status ?!Σ 1..1 code registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. code Σ 1..1 CodeableConcept Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. focus Σ 1..1 Reference(Resource) What the observation is about, when it is not about the subject of record Slices for component Σ 7..* BackboneElement Component results Slice: Unordered, Open by value:code component:All Slices Content/Rules for all slices modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. component:assay_strategy Σ 1..1 BackboneElement Component results modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: AssayStrategy value[x] Σ 0..1 CodeableConcept Actual component result component:platform_instrument Σ 1..1 BackboneElement Component results modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: PlatformInstrument value[x] Σ 0..1 CodeableConcept Actual component result component:library_prep Σ 1..1 BackboneElement Component results modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: LibraryPrep value[x] Σ 0..1 CodeableConcept Actual component result component:library_selection Σ 1..1 BackboneElement Component results modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: LibrarySelection value[x] Σ 0..1 CodeableConcept Actual component result component:strandedness Σ 1..1 BackboneElement Component results modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: Strandedness value[x] Σ 0..1 CodeableConcept Actual component result component:target_region Σ 0..1 BackboneElement Component results modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: TargetRegion value[x] Σ 0..1 CodeableConcept Actual component result component:is_paired_end Σ 1..1 BackboneElement Component results modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: IsPairedEnd value[x] Σ 0..1 Actual component result valueCodeableConcept CodeableConcept valueBoolean boolean component:adaptor_trimmed Σ 1..1 BackboneElement Component results modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: AdaptorTrimmed value[x] Σ 0..1 Actual component result valueCodeableConcept CodeableConcept valueBoolean boolean component:reference_genome Σ 0..1 BackboneElement Component results modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: ReferenceGenome value[x] Σ 0..1 CodeableConcept Actual component result component:workflow_type Σ 0..1 BackboneElement Component results modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: WorkflowType value[x] Σ 0..1 CodeableConcept Actual component result component:workflow_tool Σ 0..1 BackboneElement Component results modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) code 1..1 code Symbol in syntax defined by the system Fixed Value: WorkflowTool value[x] Σ 0..1 CodeableConcept Actual component result Documentation for this format Terminology Bindings Path Conformance ValueSet / Code URI Observation.status required ObservationStatus http://hl7.org/fhir/ValueSet/observation-status|4.3.0 from the FHIR Standard Observation.code example LOINCCodes (a valid code from LOINC) http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component.code example LOINCCodes (a valid code from LOINC) http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:assay_strategy.code example Pattern: AssayStrategy http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:platform_instrument.code example Pattern: PlatformInstrument http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:library_prep.code example Pattern: LibraryPrep http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:library_selection.code example Pattern: LibrarySelection http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:strandedness.code example Pattern: Strandedness http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:target_region.code example Pattern: TargetRegion http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:is_paired_end.code example Pattern: IsPairedEnd http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:adaptor_trimmed.code example Pattern: AdaptorTrimmed http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:reference_genome.code example Pattern: ReferenceGenome http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:workflow_type.code example Pattern: WorkflowType http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:workflow_tool.code example Pattern: WorkflowTool http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Constraints Id Grade Path(s) Details Requirements dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where(((id.exists() and ('#'+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(uri) = '#').exists()).not()).trace('unmatched', id).empty() dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() dom-6 best practice Observation A resource should have narrative for robust management : text.`div`.exists() ele-1 error **ALL** elements All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) ext-1 error **ALL** extensions Must have either extensions or value[x], not both : extension.exists() != value.exists() obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() obs-7 error Observation If 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() Snapshot View Name Flags Card. Type Description & Constraints Observation C 0..* NcpiFileMetadata Measurements and simple assertions obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present id Σ 0..1 id Logical id of this artifact meta Σ 0..1 Meta Metadata about the resource implicitRules ?!Σ 0..1 uri A set of rules under which this content was created language 0..1 code Language of the resource content Binding: CommonLanguages (preferred): IETF language tag Additional Bindings Purpose AllLanguages Max Binding text 0..1 Narrative Text summary of the resource, for human interpretation contained 0..* Resource Contained, inline Resources dom-r4b: Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url specimen-collection 0..* Reference() Linkage for related samples URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection modifierExtension ?! 0..* Extension Extensions that cannot be ignored identifier Σ 0..* Identifier Business Identifier for observation basedOn Σ 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) Part of referenced event status ?!Σ 1..1 code registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. category 0..* CodeableConcept Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. code Σ 1..1 CodeableConcept Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. subject Σ 0..1 Reference(Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance) Who and/or what the observation is about focus Σ 1..1 Reference(Resource) What the observation is about, when it is not about the subject of record encounter Σ 0..1 Reference(Encounter) Healthcare event during which this observation is made effective[x] Σ 0..1 Clinically relevant time/time-period for observation effectiveDateTime dateTime effectivePeriod Period effectiveTiming Timing effectiveInstant instant issued Σ 0..1 instant Date/Time this version was made available performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Who is responsible for the observation value[x] ΣC 0..1 Actual result valueQuantity Quantity valueCodeableConcept CodeableConcept valueString string valueBoolean boolean valueInteger integer valueRange Range valueRatio Ratio valueSampledData SampledData valueTime time valueDateTime dateTime valuePeriod Period dataAbsentReason C 0..1 CodeableConcept Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. note 0..* Annotation Comments about the observation bodySite 0..1 CodeableConcept Observed body part Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts method 0..1 CodeableConcept How it was done Binding: ObservationMethods (example): Methods for simple observations. specimen 0..1 Reference(Specimen) Specimen used for this observation device 0..1 Reference(Device | DeviceMetric) (Measurement) Device referenceRange C 0..* BackboneElement Provides guide for interpretation obs-3: Must have at least a low or a high or text id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized low C 0..1 SimpleQuantity Low Range, if relevant high C 0..1 SimpleQuantity High Range, if relevant type 0..1 CodeableConcept Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range. appliesTo 0..* CodeableConcept Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to. age 0..1 Range Applicable age range, if relevant text 0..1 string Text based reference range in an observation hasMember Σ 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Related resource that belongs to the Observation group derivedFrom Σ 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from Slices for component Σ 7..* BackboneElement Component results Slice: Unordered, Open by value:code component:All Slices Content/Rules for all slices id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. value[x] Σ 0..1 Actual component result valueQuantity Quantity valueCodeableConcept CodeableConcept valueString string valueBoolean boolean valueInteger integer valueRange Range valueRatio Ratio valueSampledData SampledData valueTime time valueDateTime dateTime valuePeriod Period dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:assay_strategy Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: AssayStrategy display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:platform_instrument Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: PlatformInstrument display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:library_prep Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: LibraryPrep display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:library_selection Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: LibrarySelection display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:strandedness Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: Strandedness display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:target_region Σ 0..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: TargetRegion display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:is_paired_end Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: IsPairedEnd display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 Actual component result valueCodeableConcept CodeableConcept valueBoolean boolean dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:adaptor_trimmed Σ 1..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: AdaptorTrimmed display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 Actual component result valueCodeableConcept CodeableConcept valueBoolean boolean dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:reference_genome Σ 0..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: ReferenceGenome display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:workflow_type Σ 0..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: WorkflowType display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result component:workflow_tool Σ 0..1 BackboneElement Component results id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized code Σ 1..1 CodeableConcept Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations coding 1..* Coding Code defined by a terminology system Fixed Value: (complex) id 0..1 string Unique id for inter-element referencing extension 0..* Extension Additional content defined by implementations system 0..1 uri Identity of the terminology system version 0..1 string Version of the system - if relevant code 1..1 code Symbol in syntax defined by the system Fixed Value: WorkflowTool display 0..1 string Representation defined by the system userSelected 0..1 boolean If this coding was chosen directly by the user text 0..1 string Plain text representation of the concept value[x] Σ 0..1 CodeableConcept Actual component result dataAbsentReason C 0..1 CodeableConcept Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. interpretation 0..* CodeableConcept High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result Documentation for this format Terminology Bindings Constraints Path Conformance ValueSet / Code URI Observation.language preferred CommonLanguages Additional Bindings Purpose AllLanguages Max Binding http://hl7.org/fhir/ValueSet/languages from the FHIR Standard Observation.status required ObservationStatus http://hl7.org/fhir/ValueSet/observation-status|4.3.0 from the FHIR Standard Observation.category preferred ObservationCategoryCodes http://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard Observation.code example LOINCCodes (a valid code from LOINC) http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.bodySite example SNOMEDCTBodyStructures http://hl7.org/fhir/ValueSet/body-site from the FHIR Standard Observation.method example ObservationMethods http://hl7.org/fhir/ValueSet/observation-methods from the FHIR Standard Observation.referenceRange.type preferred ObservationReferenceRangeMeaningCodes http://hl7.org/fhir/ValueSet/referencerange-meaning from the FHIR Standard Observation.referenceRange.appliesTo example ObservationReferenceRangeAppliesToCodes http://hl7.org/fhir/ValueSet/referencerange-appliesto from the FHIR Standard Observation.component.code example LOINCCodes (a valid code from LOINC) http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:assay_strategy.code example Pattern: AssayStrategy http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:assay_strategy.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:assay_strategy.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:platform_instrument.code example Pattern: PlatformInstrument http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:platform_instrument.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:platform_instrument.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:library_prep.code example Pattern: LibraryPrep http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:library_prep.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:library_prep.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:library_selection.code example Pattern: LibrarySelection http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:library_selection.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:library_selection.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:strandedness.code example Pattern: Strandedness http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:strandedness.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:strandedness.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:target_region.code example Pattern: TargetRegion http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:target_region.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:target_region.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:is_paired_end.code example Pattern: IsPairedEnd http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:is_paired_end.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:is_paired_end.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:adaptor_trimmed.code example Pattern: AdaptorTrimmed http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:adaptor_trimmed.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:adaptor_trimmed.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:reference_genome.code example Pattern: ReferenceGenome http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:reference_genome.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:reference_genome.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:workflow_type.code example Pattern: WorkflowType http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:workflow_type.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:workflow_type.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Observation.component:workflow_tool.code example Pattern: WorkflowTool http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard Observation.component:workflow_tool.dataAbsentReason extensible DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard Observation.component:workflow_tool.interpretation extensible ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard Id Grade Path(s) Details Requirements dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where(((id.exists() and ('#'+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(uri) = '#').exists()).not()).trace('unmatched', id).empty() dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() dom-6 best practice Observation A resource should have narrative for robust management : text.`div`.exists() dom-r4b warning Observation.contained Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems : ($this is Citation or $this is Evidence or $this is EvidenceReport or $this is EvidenceVariable or $this is MedicinalProductDefinition or $this is PackagedProductDefinition or $this is AdministrableProductDefinition or $this is Ingredient or $this is ClinicalUseDefinition or $this is RegulatedAuthorization or $this is SubstanceDefinition or $this is SubscriptionStatus or $this is SubscriptionTopic) implies (%resource is Citation or %resource is Evidence or %resource is EvidenceReport or %resource is EvidenceVariable or %resource is MedicinalProductDefinition or %resource is PackagedProductDefinition or %resource is AdministrableProductDefinition or %resource is Ingredient or %resource is ClinicalUseDefinition or %resource is RegulatedAuthorization or %resource is SubstanceDefinition or %resource is SubscriptionStatus or %resource is SubscriptionTopic) ele-1 error **ALL** elements All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) ext-1 error **ALL** extensions Must have either extensions or value[x], not both : extension.exists() != value.exists() obs-3 error Observation.referenceRange Must have at least a low or a high or text : low.exists() or high.exists() or text.exists() obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() obs-7 error Observation If 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() This structure is derived from NcpiFileMetadata Summary Mandatory: 7 elements Extensions This structure refers to these extensions: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/specimen-collection Slices This structure defines the following Slices: The element 1 is sliced based on the value of Observation.component   Other representations of profile: CSV, Excel, Schematron IG © 2023+ NCPI FHIR Working Group. Package ncpi-fhir-implementation-guide-v2#0.1.0 based on FHIR 4.3.0. Generated 2024-11-25 Links: Table of Contents | QA Report