Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

Resource Profile: Genomic Finding ( Abstract )

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/finding Version: 4.0.0-cibuild
Standards status: Trial-use Maturity Level: 2 Computable Name: GenomicFinding

Copyright/Legal: This material contains content from LOINC (http://loinc.org). LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc.

Properties common to genetic findings whose results are expressed as computable discrete elements (e.g. genotypes, haplotypes, variants, etc.).

Scope and Usage

The primary focus of genomic testing is making Genomic Findings. These are the fine and/or coarse-grained descriptions of a specimen's genomic characteristics. This profile is the base profile for all other finding profiles, defining a set of constraints that are applicable across all findings.

Class diagram showing relationship of genomic findings as well as genotypes, haplotypes, variants and sequences.

Genomic Findings

Genomic Finding, Genotype, Haplotype, Variant (or see Variant Reporting), Sequence Phase Relationship

Types of Findings

  • Genotypes describe combinations of genomic variations that together are associated with a particular phenotype - i.e., a specific physical, behavioral, or risk-associated difference associated with the organism whose specimen was tested.
  • Haplotypes describe a set of genomic variations that appear on a single strand of DNA - and which are therefore typically inherited together
  • Variants are specific differences or combinations of differences between parts of one or more specimen sequences and the equivalent portions of the reference sequence(s) for that organism. The Variant Reporting section deals with all types of variants detected by formal sequencing, including simple/discrete variants, structural variants and complex variants detected by direct sequencing, shotgun-based sequencing, and array-based testing for specific variants.
  • Sequence Phase Relationships describe the CIS or TRANS relationship of findings.

These categories of observations have relationships. Haplotypes can be identified based on the presence of variants. Genotypes can be identified based on the presence of haplotypes and/or variants. All three can be expressed as a combination of one or more sequences.

Common Elements

  • reference-sequence-assembly (component) represents reference sequence used when determining this finding
  • chromosome-identifier (component) represents the chromosome for the finding
  • cytogenetic-location (component) represents the chromosome, arm, and band (can be multiple) for the finding
  • gene-studied (component) represents the gene(s) for the finding.

Usages:

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

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

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicBase This is an abstract profile. Child profiles: Variant, Haplotype, SequencePhaseRelationship, Genotype
Measurements and simple assertions
Constraints: obs-6, obs-7
Observation.implicitRules This element is a modifier element. This element is included in summaries. 0..1 uri A set of rules under which this content was created
Observation.Slices for extension Content/Rules for all slices
Observation.Slices for extension.extension:secondary-finding 0..1 CodeableConcept Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
Observation.Slices for extension.extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
Observation.modifierExtension This element is a modifier element. 0..* Extension Extensions that cannot be ignored
Observation.status This element is a modifier element. This element is included in summaries. 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
Observation.Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
  "code" : "laboratory"
}
Observation.Slices for category.category:geCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:geCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
Observation.code This element is included in summaries. 1..1 CodeableConcept Type of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.derivedFrom This element is included in summaries. 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
Observation.Slices for component This element is included in summaries. 0..* BackboneElement Component results
Slice: Unordered, Open by value:code
Observation.Slices for component.component:All Slices Content/Rules for all slices
Observation.Slices for component.component:All Slices.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:All Slices.code This element is included in summaries. 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.Slices for component.component:conclusion-string This element is included in summaries. 0..1 BackboneElement Clinical Conclusion
Observation.Slices for component.component:conclusion-string.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:conclusion-string.code This element is included in summaries. 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "conclusion-string"
    }
  ]
}
Observation.Slices for component.component:gene-studied This element is included in summaries. 0..* BackboneElement Gene Studied
Observation.Slices for component.component:gene-studied.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:gene-studied.code This element is included in summaries. 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48018-6"
    }
  ]
}
Observation.Slices for component.component:gene-studied.value[x] This element is included in summaries. 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
Observation.Slices for component.component:cytogenetic-location This element is included in summaries. 0..* BackboneElement Cytogenetic (Chromosome) Location
Observation.Slices for component.component:cytogenetic-location.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:cytogenetic-location.code This element is included in summaries. 1..1 CodeableConcept 48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48001-2"
    }
  ]
}
Observation.Slices for component.component:cytogenetic-location.value[x] This element is included in summaries. 1..1 CodeableConcept Example: 1q21.1
Observation.Slices for component.component:reference-sequence-assembly This element is included in summaries. 0..* BackboneElement Human Reference Sequence Assembly
Observation.Slices for component.component:reference-sequence-assembly.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:reference-sequence-assembly.code This element is included in summaries. 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "62374-4"
    }
  ]
}
Observation.Slices for component.component:reference-sequence-assembly.value[x] This element is included in summaries. 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
Observation.Slices for component.component:chromosome-identifier This element is included in summaries. 0..* BackboneElement Chromosome Identifier
Observation.Slices for component.component:chromosome-identifier.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:chromosome-identifier.code This element is included in summaries. 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48000-4"
    }
  ]
}
Observation.Slices for component.component:chromosome-identifier.value[x] This element is included in summaries. 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:geCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-cibuild This IG
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 ∅ unknown?
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 ∅ unknown?

Constraints

Id Grade Path(s) Description Expression
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 in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-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()

This structure is derived from GenomicBase

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation 0..* GenomicBase This is an abstract profile. Child profiles: Variant, Haplotype, SequencePhaseRelationship, Genotype
Measurements and simple assertions
Observation.Slices for component Content/Rules for all slices
Observation.Slices for component.component:gene-studied 0..* BackboneElement Gene Studied
Observation.Slices for component.component:gene-studied.code 1..1 CodeableConcept 48018-6
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48018-6"
    }
  ]
}
Observation.Slices for component.component:gene-studied.value[x] 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
Observation.Slices for component.component:cytogenetic-location 0..* BackboneElement Cytogenetic (Chromosome) Location
Observation.Slices for component.component:cytogenetic-location.code 1..1 CodeableConcept 48001-2
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48001-2"
    }
  ]
}
Observation.Slices for component.component:cytogenetic-location.value[x] 1..1 CodeableConcept Example: 1q21.1
Observation.Slices for component.component:reference-sequence-assembly 0..* BackboneElement Human Reference Sequence Assembly
Observation.Slices for component.component:reference-sequence-assembly.code 1..1 CodeableConcept 62374-4
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "62374-4"
    }
  ]
}
Observation.Slices for component.component:reference-sequence-assembly.value[x] 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
Observation.Slices for component.component:chromosome-identifier 0..* BackboneElement Chromosome Identifier
Observation.Slices for component.component:chromosome-identifier.code 1..1 CodeableConcept 48000-4
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48000-4"
    }
  ]
}
Observation.Slices for component.component:chromosome-identifier.value[x] 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-cibuild This IG
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 ∅ unknown?
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 ∅ unknown?
NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicBase This is an abstract profile. Child profiles: Variant, Haplotype, SequencePhaseRelationship, Genotype
Measurements and simple assertions
Constraints: obs-6, obs-7
Observation.id This element is included in summaries. 0..1 id Logical id of this artifact
Observation.meta This element is included in summaries. 0..1 Meta Metadata about the resource
Observation.implicitRules This element is a modifier element. This element is included in summaries. 0..1 uri A set of rules under which this content was created
Observation.language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.
Additional BindingsPurpose
AllLanguages Max Binding
Observation.text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
Observation.contained 0..* Resource Contained, inline Resources
Observation.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for extension.extension:secondary-finding 0..1 CodeableConcept Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
Observation.Slices for extension.extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
Observation.modifierExtension This element is a modifier element. 0..* Extension Extensions that cannot be ignored
Observation.identifier This element is included in summaries. 0..* Identifier Business Identifier for observation
Observation.basedOn This element is included in summaries. 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
Observation.partOf This element is included in summaries. 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) Part of referenced event
Observation.status This element is a modifier element. This element is included in summaries. 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
Observation.Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory.id 0..1 string Unique id for inter-element referencing
Observation.Slices for category.category:labCategory.extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Observation.Slices for category.category:labCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
  "code" : "laboratory"
}
Observation.Slices for category.category:labCategory.text This element is included in summaries. 0..1 string Plain text representation of the concept
Observation.Slices for category.category:geCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:geCategory.id 0..1 string Unique id for inter-element referencing
Observation.Slices for category.category:geCategory.extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Observation.Slices for category.category:geCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
Observation.Slices for category.category:geCategory.text This element is included in summaries. 0..1 string Plain text representation of the concept
Observation.code This element is included in summaries. 1..1 CodeableConcept Type of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.subject This element is included in summaries. 0..1 Reference(Patient | Group | Device | Location) Who and/or what the observation is about
Observation.focus This element is included in summaries. 0..* Reference(Resource) What the observation is about, when it is not about the subject of record
Observation.encounter This element is included in summaries. 0..1 Reference(Encounter) Healthcare event during which this observation is made
Observation.effective[x] This element is included in summaries. 0..1 Clinically relevant time/time-period for observation
Observation.effective[x].effectiveDateTime dateTime
Observation.effective[x].effectivePeriod Period
Observation.effective[x].effectiveTiming Timing
Observation.effective[x].effectiveInstant instant
Observation.issued This element is included in summaries. 0..1 instant Date/Time this version was made available
Observation.performer This element is included in summaries. 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Who is responsible for the observation
Observation.value[x] This element is included in summaries. C 0..1 Actual result
Observation.value[x].valueQuantity Quantity
Observation.value[x].valueCodeableConcept CodeableConcept
Observation.value[x].valueString string
Observation.value[x].valueBoolean boolean
Observation.value[x].valueInteger integer
Observation.value[x].valueRange Range
Observation.value[x].valueRatio Ratio
Observation.value[x].valueSampledData SampledData
Observation.value[x].valueTime time
Observation.value[x].valueDateTime dateTime
Observation.value[x].valuePeriod Period
Observation.dataAbsentReason C 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.note 0..* CodedAnnotation Comments about the Observation that also contain a coded type
Observation.bodySite 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
Observation.method 0..1 CodeableConcept How it was done
Binding: ObservationMethods (example): Methods for simple observations.
Observation.specimen 0..1 Reference(Specimen) Specimen used for this observation
Observation.device 0..1 Reference(Device | DeviceMetric) (Measurement) Device
Observation.referenceRange C 0..* BackboneElement Provides guide for interpretation
Constraints: obs-3
Observation.referenceRange.id 0..1 string Unique id for inter-element referencing
Observation.referenceRange.extension 0..* Extension Additional content defined by implementations
Observation.referenceRange.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.referenceRange.low C 0..1 SimpleQuantity(4.0.1) Low Range, if relevant
Constraints: sqty-1
Observation.referenceRange.high C 0..1 SimpleQuantity(4.0.1) High Range, if relevant
Constraints: sqty-1
Observation.referenceRange.type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
Observation.referenceRange.appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
Observation.referenceRange.age 0..1 Range Applicable age range, if relevant
Observation.referenceRange.text 0..1 string Text based reference range in an observation
Observation.hasMember This element is included in summaries. 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Related resource that belongs to the Observation group
Observation.derivedFrom This element is included in summaries. 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
Observation.Slices for component This element is included in summaries. 0..* BackboneElement Component results
Slice: Unordered, Open by value:code
Observation.Slices for component.component:All Slices Content/Rules for all slices
Observation.Slices for component.component:All Slices.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:All Slices.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:All Slices.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:All Slices.code This element is included in summaries. 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.Slices for component.component:All Slices.value[x] This element is included in summaries. 0..1 Actual component result
Observation.Slices for component.component:All Slices.value[x].valueQuantity Quantity
Observation.Slices for component.component:All Slices.value[x].valueCodeableConcept CodeableConcept
Observation.Slices for component.component:All Slices.value[x].valueString string
Observation.Slices for component.component:All Slices.value[x].valueBoolean boolean
Observation.Slices for component.component:All Slices.value[x].valueInteger integer
Observation.Slices for component.component:All Slices.value[x].valueRange Range
Observation.Slices for component.component:All Slices.value[x].valueRatio Ratio
Observation.Slices for component.component:All Slices.value[x].valueSampledData SampledData
Observation.Slices for component.component:All Slices.value[x].valueTime time
Observation.Slices for component.component:All Slices.value[x].valueDateTime dateTime
Observation.Slices for component.component:All Slices.value[x].valuePeriod Period
Observation.Slices for component.component:All Slices.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:All Slices.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:All Slices.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:conclusion-string This element is included in summaries. 0..1 BackboneElement Clinical Conclusion
Observation.Slices for component.component:conclusion-string.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:conclusion-string.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:conclusion-string.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:conclusion-string.code This element is included in summaries. 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "conclusion-string"
    }
  ]
}
Observation.Slices for component.component:conclusion-string.value[x] This element is included in summaries. 0..1 string Summary conclusion (interpretation/impression)
Observation.Slices for component.component:conclusion-string.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:conclusion-string.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:conclusion-string.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:gene-studied This element is included in summaries. 0..* BackboneElement Gene Studied
Observation.Slices for component.component:gene-studied.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:gene-studied.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:gene-studied.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:gene-studied.code This element is included in summaries. 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48018-6"
    }
  ]
}
Observation.Slices for component.component:gene-studied.value[x] This element is included in summaries. 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
Observation.Slices for component.component:gene-studied.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:gene-studied.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:gene-studied.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:cytogenetic-location This element is included in summaries. 0..* BackboneElement Cytogenetic (Chromosome) Location
Observation.Slices for component.component:cytogenetic-location.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:cytogenetic-location.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:cytogenetic-location.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:cytogenetic-location.code This element is included in summaries. 1..1 CodeableConcept 48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48001-2"
    }
  ]
}
Observation.Slices for component.component:cytogenetic-location.value[x] This element is included in summaries. 1..1 CodeableConcept Example: 1q21.1
Observation.Slices for component.component:cytogenetic-location.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:cytogenetic-location.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:cytogenetic-location.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:reference-sequence-assembly This element is included in summaries. 0..* BackboneElement Human Reference Sequence Assembly
Observation.Slices for component.component:reference-sequence-assembly.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:reference-sequence-assembly.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:reference-sequence-assembly.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:reference-sequence-assembly.code This element is included in summaries. 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "62374-4"
    }
  ]
}
Observation.Slices for component.component:reference-sequence-assembly.value[x] This element is included in summaries. 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
Observation.Slices for component.component:reference-sequence-assembly.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:reference-sequence-assembly.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:reference-sequence-assembly.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:chromosome-identifier This element is included in summaries. 0..* BackboneElement Chromosome Identifier
Observation.Slices for component.component:chromosome-identifier.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:chromosome-identifier.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:chromosome-identifier.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:chromosome-identifier.code This element is included in summaries. 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48000-4"
    }
  ]
}
Observation.Slices for component.component:chromosome-identifier.value[x] This element is included in summaries. 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
Observation.Slices for component.component:chromosome-identifier.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:chromosome-identifier.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:chromosome-identifier.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.language Base preferred Common Languages 📍4.0.1 FHIR Std.
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:geCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.bodySite Base example SNOMED CT Body Structures 📍4.0.1 FHIR Std.
Observation.method Base example Observation Methods 📍4.0.1 FHIR Std.
Observation.referenceRange.​type Base preferred Observation Reference Range Meaning Codes 📍4.0.1 FHIR Std.
Observation.referenceRange.​appliesTo Base example Observation Reference Range Applies To Codes 📍4.0.1 FHIR Std.
Observation.component.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-cibuild This IG
Observation.component:gene-studied.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 ∅ unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 ∅ unknown?
Observation.component:chromosome-identifier.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
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 in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-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-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()
sqty-1 error Observation.referenceRange.low, Observation.referenceRange.high The comparator is not used on a SimpleQuantity comparator.empty()

This structure is derived from GenomicBase

Summary

Mandatory: 0 element(4 nested mandatory elements)

Maturity: 2

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicBase This is an abstract profile. Child profiles: Variant, Haplotype, SequencePhaseRelationship, Genotype
Measurements and simple assertions
Constraints: obs-6, obs-7
Observation.implicitRules This element is a modifier element. This element is included in summaries. 0..1 uri A set of rules under which this content was created
Observation.Slices for extension Content/Rules for all slices
Observation.Slices for extension.extension:secondary-finding 0..1 CodeableConcept Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
Observation.Slices for extension.extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
Observation.modifierExtension This element is a modifier element. 0..* Extension Extensions that cannot be ignored
Observation.status This element is a modifier element. This element is included in summaries. 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
Observation.Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
  "code" : "laboratory"
}
Observation.Slices for category.category:geCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:geCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
Observation.code This element is included in summaries. 1..1 CodeableConcept Type of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.derivedFrom This element is included in summaries. 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
Observation.Slices for component This element is included in summaries. 0..* BackboneElement Component results
Slice: Unordered, Open by value:code
Observation.Slices for component.component:All Slices Content/Rules for all slices
Observation.Slices for component.component:All Slices.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:All Slices.code This element is included in summaries. 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.Slices for component.component:conclusion-string This element is included in summaries. 0..1 BackboneElement Clinical Conclusion
Observation.Slices for component.component:conclusion-string.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:conclusion-string.code This element is included in summaries. 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "conclusion-string"
    }
  ]
}
Observation.Slices for component.component:gene-studied This element is included in summaries. 0..* BackboneElement Gene Studied
Observation.Slices for component.component:gene-studied.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:gene-studied.code This element is included in summaries. 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48018-6"
    }
  ]
}
Observation.Slices for component.component:gene-studied.value[x] This element is included in summaries. 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
Observation.Slices for component.component:cytogenetic-location This element is included in summaries. 0..* BackboneElement Cytogenetic (Chromosome) Location
Observation.Slices for component.component:cytogenetic-location.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:cytogenetic-location.code This element is included in summaries. 1..1 CodeableConcept 48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48001-2"
    }
  ]
}
Observation.Slices for component.component:cytogenetic-location.value[x] This element is included in summaries. 1..1 CodeableConcept Example: 1q21.1
Observation.Slices for component.component:reference-sequence-assembly This element is included in summaries. 0..* BackboneElement Human Reference Sequence Assembly
Observation.Slices for component.component:reference-sequence-assembly.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:reference-sequence-assembly.code This element is included in summaries. 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "62374-4"
    }
  ]
}
Observation.Slices for component.component:reference-sequence-assembly.value[x] This element is included in summaries. 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
Observation.Slices for component.component:chromosome-identifier This element is included in summaries. 0..* BackboneElement Chromosome Identifier
Observation.Slices for component.component:chromosome-identifier.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:chromosome-identifier.code This element is included in summaries. 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48000-4"
    }
  ]
}
Observation.Slices for component.component:chromosome-identifier.value[x] This element is included in summaries. 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:geCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-cibuild This IG
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 ∅ unknown?
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 ∅ unknown?

Constraints

Id Grade Path(s) Description Expression
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 in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-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()

Differential View

This structure is derived from GenomicBase

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation 0..* GenomicBase This is an abstract profile. Child profiles: Variant, Haplotype, SequencePhaseRelationship, Genotype
Measurements and simple assertions
Observation.Slices for component Content/Rules for all slices
Observation.Slices for component.component:gene-studied 0..* BackboneElement Gene Studied
Observation.Slices for component.component:gene-studied.code 1..1 CodeableConcept 48018-6
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48018-6"
    }
  ]
}
Observation.Slices for component.component:gene-studied.value[x] 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
Observation.Slices for component.component:cytogenetic-location 0..* BackboneElement Cytogenetic (Chromosome) Location
Observation.Slices for component.component:cytogenetic-location.code 1..1 CodeableConcept 48001-2
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48001-2"
    }
  ]
}
Observation.Slices for component.component:cytogenetic-location.value[x] 1..1 CodeableConcept Example: 1q21.1
Observation.Slices for component.component:reference-sequence-assembly 0..* BackboneElement Human Reference Sequence Assembly
Observation.Slices for component.component:reference-sequence-assembly.code 1..1 CodeableConcept 62374-4
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "62374-4"
    }
  ]
}
Observation.Slices for component.component:reference-sequence-assembly.value[x] 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
Observation.Slices for component.component:chromosome-identifier 0..* BackboneElement Chromosome Identifier
Observation.Slices for component.component:chromosome-identifier.code 1..1 CodeableConcept 48000-4
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48000-4"
    }
  ]
}
Observation.Slices for component.component:chromosome-identifier.value[x] 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-cibuild This IG
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 ∅ unknown?
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 ∅ unknown?

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicBase This is an abstract profile. Child profiles: Variant, Haplotype, SequencePhaseRelationship, Genotype
Measurements and simple assertions
Constraints: obs-6, obs-7
Observation.id This element is included in summaries. 0..1 id Logical id of this artifact
Observation.meta This element is included in summaries. 0..1 Meta Metadata about the resource
Observation.implicitRules This element is a modifier element. This element is included in summaries. 0..1 uri A set of rules under which this content was created
Observation.language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.
Additional BindingsPurpose
AllLanguages Max Binding
Observation.text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
Observation.contained 0..* Resource Contained, inline Resources
Observation.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for extension.extension:secondary-finding 0..1 CodeableConcept Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
Observation.Slices for extension.extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
Observation.modifierExtension This element is a modifier element. 0..* Extension Extensions that cannot be ignored
Observation.identifier This element is included in summaries. 0..* Identifier Business Identifier for observation
Observation.basedOn This element is included in summaries. 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
Observation.partOf This element is included in summaries. 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) Part of referenced event
Observation.status This element is a modifier element. This element is included in summaries. 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
Observation.Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory.id 0..1 string Unique id for inter-element referencing
Observation.Slices for category.category:labCategory.extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Observation.Slices for category.category:labCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
  "code" : "laboratory"
}
Observation.Slices for category.category:labCategory.text This element is included in summaries. 0..1 string Plain text representation of the concept
Observation.Slices for category.category:geCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:geCategory.id 0..1 string Unique id for inter-element referencing
Observation.Slices for category.category:geCategory.extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Observation.Slices for category.category:geCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
Observation.Slices for category.category:geCategory.text This element is included in summaries. 0..1 string Plain text representation of the concept
Observation.code This element is included in summaries. 1..1 CodeableConcept Type of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.subject This element is included in summaries. 0..1 Reference(Patient | Group | Device | Location) Who and/or what the observation is about
Observation.focus This element is included in summaries. 0..* Reference(Resource) What the observation is about, when it is not about the subject of record
Observation.encounter This element is included in summaries. 0..1 Reference(Encounter) Healthcare event during which this observation is made
Observation.effective[x] This element is included in summaries. 0..1 Clinically relevant time/time-period for observation
Observation.effective[x].effectiveDateTime dateTime
Observation.effective[x].effectivePeriod Period
Observation.effective[x].effectiveTiming Timing
Observation.effective[x].effectiveInstant instant
Observation.issued This element is included in summaries. 0..1 instant Date/Time this version was made available
Observation.performer This element is included in summaries. 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Who is responsible for the observation
Observation.value[x] This element is included in summaries. C 0..1 Actual result
Observation.value[x].valueQuantity Quantity
Observation.value[x].valueCodeableConcept CodeableConcept
Observation.value[x].valueString string
Observation.value[x].valueBoolean boolean
Observation.value[x].valueInteger integer
Observation.value[x].valueRange Range
Observation.value[x].valueRatio Ratio
Observation.value[x].valueSampledData SampledData
Observation.value[x].valueTime time
Observation.value[x].valueDateTime dateTime
Observation.value[x].valuePeriod Period
Observation.dataAbsentReason C 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.note 0..* CodedAnnotation Comments about the Observation that also contain a coded type
Observation.bodySite 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
Observation.method 0..1 CodeableConcept How it was done
Binding: ObservationMethods (example): Methods for simple observations.
Observation.specimen 0..1 Reference(Specimen) Specimen used for this observation
Observation.device 0..1 Reference(Device | DeviceMetric) (Measurement) Device
Observation.referenceRange C 0..* BackboneElement Provides guide for interpretation
Constraints: obs-3
Observation.referenceRange.id 0..1 string Unique id for inter-element referencing
Observation.referenceRange.extension 0..* Extension Additional content defined by implementations
Observation.referenceRange.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.referenceRange.low C 0..1 SimpleQuantity(4.0.1) Low Range, if relevant
Constraints: sqty-1
Observation.referenceRange.high C 0..1 SimpleQuantity(4.0.1) High Range, if relevant
Constraints: sqty-1
Observation.referenceRange.type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
Observation.referenceRange.appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
Observation.referenceRange.age 0..1 Range Applicable age range, if relevant
Observation.referenceRange.text 0..1 string Text based reference range in an observation
Observation.hasMember This element is included in summaries. 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Related resource that belongs to the Observation group
Observation.derivedFrom This element is included in summaries. 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
Observation.Slices for component This element is included in summaries. 0..* BackboneElement Component results
Slice: Unordered, Open by value:code
Observation.Slices for component.component:All Slices Content/Rules for all slices
Observation.Slices for component.component:All Slices.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:All Slices.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:All Slices.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:All Slices.code This element is included in summaries. 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.Slices for component.component:All Slices.value[x] This element is included in summaries. 0..1 Actual component result
Observation.Slices for component.component:All Slices.value[x].valueQuantity Quantity
Observation.Slices for component.component:All Slices.value[x].valueCodeableConcept CodeableConcept
Observation.Slices for component.component:All Slices.value[x].valueString string
Observation.Slices for component.component:All Slices.value[x].valueBoolean boolean
Observation.Slices for component.component:All Slices.value[x].valueInteger integer
Observation.Slices for component.component:All Slices.value[x].valueRange Range
Observation.Slices for component.component:All Slices.value[x].valueRatio Ratio
Observation.Slices for component.component:All Slices.value[x].valueSampledData SampledData
Observation.Slices for component.component:All Slices.value[x].valueTime time
Observation.Slices for component.component:All Slices.value[x].valueDateTime dateTime
Observation.Slices for component.component:All Slices.value[x].valuePeriod Period
Observation.Slices for component.component:All Slices.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:All Slices.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:All Slices.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:conclusion-string This element is included in summaries. 0..1 BackboneElement Clinical Conclusion
Observation.Slices for component.component:conclusion-string.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:conclusion-string.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:conclusion-string.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:conclusion-string.code This element is included in summaries. 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "conclusion-string"
    }
  ]
}
Observation.Slices for component.component:conclusion-string.value[x] This element is included in summaries. 0..1 string Summary conclusion (interpretation/impression)
Observation.Slices for component.component:conclusion-string.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:conclusion-string.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:conclusion-string.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:gene-studied This element is included in summaries. 0..* BackboneElement Gene Studied
Observation.Slices for component.component:gene-studied.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:gene-studied.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:gene-studied.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:gene-studied.code This element is included in summaries. 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48018-6"
    }
  ]
}
Observation.Slices for component.component:gene-studied.value[x] This element is included in summaries. 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
Observation.Slices for component.component:gene-studied.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:gene-studied.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:gene-studied.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:cytogenetic-location This element is included in summaries. 0..* BackboneElement Cytogenetic (Chromosome) Location
Observation.Slices for component.component:cytogenetic-location.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:cytogenetic-location.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:cytogenetic-location.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:cytogenetic-location.code This element is included in summaries. 1..1 CodeableConcept 48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48001-2"
    }
  ]
}
Observation.Slices for component.component:cytogenetic-location.value[x] This element is included in summaries. 1..1 CodeableConcept Example: 1q21.1
Observation.Slices for component.component:cytogenetic-location.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:cytogenetic-location.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:cytogenetic-location.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:reference-sequence-assembly This element is included in summaries. 0..* BackboneElement Human Reference Sequence Assembly
Observation.Slices for component.component:reference-sequence-assembly.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:reference-sequence-assembly.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:reference-sequence-assembly.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:reference-sequence-assembly.code This element is included in summaries. 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "62374-4"
    }
  ]
}
Observation.Slices for component.component:reference-sequence-assembly.value[x] This element is included in summaries. 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
Observation.Slices for component.component:reference-sequence-assembly.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:reference-sequence-assembly.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:reference-sequence-assembly.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:chromosome-identifier This element is included in summaries. 0..* BackboneElement Chromosome Identifier
Observation.Slices for component.component:chromosome-identifier.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:chromosome-identifier.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:chromosome-identifier.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:chromosome-identifier.code This element is included in summaries. 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48000-4"
    }
  ]
}
Observation.Slices for component.component:chromosome-identifier.value[x] This element is included in summaries. 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
Observation.Slices for component.component:chromosome-identifier.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:chromosome-identifier.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:chromosome-identifier.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.language Base preferred Common Languages 📍4.0.1 FHIR Std.
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:geCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.bodySite Base example SNOMED CT Body Structures 📍4.0.1 FHIR Std.
Observation.method Base example Observation Methods 📍4.0.1 FHIR Std.
Observation.referenceRange.​type Base preferred Observation Reference Range Meaning Codes 📍4.0.1 FHIR Std.
Observation.referenceRange.​appliesTo Base example Observation Reference Range Applies To Codes 📍4.0.1 FHIR Std.
Observation.component.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-cibuild This IG
Observation.component:gene-studied.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 ∅ unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 ∅ unknown?
Observation.component:chromosome-identifier.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
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 in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-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-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()
sqty-1 error Observation.referenceRange.low, Observation.referenceRange.high The comparator is not used on a SimpleQuantity comparator.empty()

This structure is derived from GenomicBase

Summary

Mandatory: 0 element(4 nested mandatory elements)

Maturity: 2

 

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