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: Molecular Consequence

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

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.

Profile for communicating the calculated or observed effect of a DNA variant, generally on its downstream transcript and, if applicable, ensuing protein sequence. Molecular consequences may also apply to DNA, such as intergenic regions where there are no transcripts (e.g. 'regulatory_region_variant'). Component 'feature-consequence' categorizes the structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion), whereas component 'functional-effect' categorizes how the variant affects overall function (e.g. is predicted to result in loss of gene function).

Molecular Consequence Use Case

A given variant can have multiple transcript-specific predicted molecular consequences. Clinical applications such as rare disease variant discovery, clinical trial matching, and the determination of therapeutic options for cancer patients may need to examine each predicted consequence as part of a variant filtration and prioritization process.

Detailed Example

In this example, a variant in a gene with multiple transcripts is annotated with multiple transcript-specific molecular consequence predictions. This figure shows multiple transcripts of the ODF2L gene.

Multiple transcripts of ODF2L gene

This next figure shows a VCF row. A variant in the ODF2L gene has been annotated with the snpEff/snpSIFT variant prediction tool. Things to note include:

  • The example here prefixes the URI with http://example.org as is the standard approach in HL7 guides when a code system is not an official terminology
  • snpEff predicts a molecular consequence for each known transcript
  • Each molecular consequence has one or more 'effects' (drawn from Sequence Ontology), and an 'impact category' (HIGH, MODERATE, LOW, MODIFIER)
  • Note how variants occurring outside of exons in certain transcripts (e.g. intron_variant) do not have an associated pHGVS
  • snpEff may assign an overall 'LOF' (Loss of Function) prediction. (In these examples, we include the 'LOF' where effect=HIGH)
  • This example uses snpSIFT with gnomAD to annotate a population allele frequency
  • In some cases, snpEff will assign more than one molecular consequence to a given transcript (e.g. splice_donor_variant&intron_variant)
Predicted ODF2L molecular consequences

These following examples correspond to the annotated VCF row.

See Genomic Implication for guidance.

Differentiating AND vs OR

There are several cases where it is necessary to differentiate 'AND' conditions (e.g. a consequence of a DNA variant is both X and Y, as in the first example above where a consequence is both a 'splice_donor_variation' AND a 'intron_variant') vs. 'OR' conditions (e.g. a consequence of a DNA variant may be X or may by Y, as in the example above where a consequence might be 'synonymous variant' OR 'intron_variant'). This situation is not unique to molecular consequences, and arises elsewhere within FHIR (e.g. FHIR Search) and outside of FHIR (e.g. Clinvar submission API condition set). To be consistent with other precedents, where molecular consequences have fields with cardinality >1, the inclusion of multiple values within a field shall indicate an 'AND' condition. An 'OR' condition is represented by multiple observation instances.

See Genomic Implication for additional information. Implication fields affected by this guidance include: derivedFrom, evidence-level, feature-consequence.

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..* GenomicImplication Molecular Consequence
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.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
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 molecular-consequence
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" : "molecular-consequence"
    }
  ]
}
Observation.Slices for derivedFrom This element is included in summaries. 1..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
Observation.Slices for derivedFrom.derivedFrom:variant This element is included in summaries. 0..* Reference(Variant) Variant the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:genotype This element is included in summaries. 0..* Reference(Genotype) Genotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:haplotype This element is included in summaries. 0..* Reference(Haplotype) Haplotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:biomarker This element is included in summaries. 0..* Reference(Molecular Biomarker) MolecularBiomarker the implication is derived from
Observation.Slices for component This element is included in summaries. 0..* BackboneElement Component results
Slice: Unordered, Open by value:code

Slicing Note: The rules on this element (including its children) apply to all the slices, but are not repeated in them
Observation.Slices for component.component:All Slices Content/Rules for all slices
Observation.Slices for component.component:All Slices.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:All Slices.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
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:evidence-level This element is included in summaries. 0..* BackboneElement Level of Evidence
Observation.Slices for component.component:evidence-level.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:evidence-level.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:evidence-level.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:evidence-level.code This element is included in summaries. 1..1 CodeableConcept 93044-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "93044-6"
    }
  ]
}
Observation.Slices for component.component:evidence-level.value[x] This element is included in summaries. 1..1 CodeableConcept 1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star
Binding: Evidence Level Examples (example): PharmGKB or ClinVar
Observation.Slices for component.component:clinical-significance This element is included in summaries. 0..1 BackboneElement Clinical significance
Observation.Slices for component.component:clinical-significance.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:clinical-significance.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:clinical-significance.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:clinical-significance.code This element is included in summaries. 1..1 CodeableConcept 53037-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "53037-8"
    }
  ]
}
Observation.Slices for component.component:clinical-significance.value[x] This element is included in summaries. 1..1 CodeableConcept Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (example)
Observation.Slices for component.component:knowledge-base This element is included in summaries. 0..1 BackboneElement Knowledge Base
Observation.Slices for component.component:knowledge-base.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:knowledge-base.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:knowledge-base.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:knowledge-base.code This element is included in summaries. 1..1 CodeableConcept knowledge-base
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" : "knowledge-base"
    }
  ]
}
Observation.Slices for component.component:knowledge-base.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Binding: Knowledge Base Version Codes (example)
Observation.Slices for component.component:annotation-pipeline This element is included in summaries. 0..1 BackboneElement Annotation Pipeline
Observation.Slices for component.component:annotation-pipeline.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:annotation-pipeline.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:annotation-pipeline.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:annotation-pipeline.code This element is included in summaries. 1..1 CodeableConcept annotation-pipeline
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" : "annotation-pipeline"
    }
  ]
}
Observation.Slices for component.component:annotation-pipeline.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Observation.Slices for component.component:coding-hgvs This element is included in summaries. 0..1 BackboneElement DNA change (c.HGVS)
Observation.Slices for component.component:coding-hgvs.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:coding-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48004-6"
    }
  ]
}
Observation.Slices for component.component:coding-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:transcript-ref-seq This element is included in summaries. 0..1 BackboneElement Reference Transcript
Observation.Slices for component.component:transcript-ref-seq.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:transcript-ref-seq.code This element is included in summaries. 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51958-7"
    }
  ]
}
Observation.Slices for component.component:transcript-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:protein-hgvs This element is included in summaries. 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
Observation.Slices for component.component:protein-hgvs.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:protein-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48005-3"
    }
  ]
}
Observation.Slices for component.component:protein-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:protein-ref-seq This element is included in summaries. 0..1 BackboneElement Protein Reference Sequence
Observation.Slices for component.component:protein-ref-seq.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:protein-ref-seq.code This element is included in summaries. 1..1 CodeableConcept protein-ref-seq
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" : "protein-ref-seq"
    }
  ]
}
Observation.Slices for component.component:protein-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:feature-consequence This element is included in summaries. 0..* BackboneElement Feature Consequence
Observation.Slices for component.component:feature-consequence.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:feature-consequence.code This element is included in summaries. 1..1 CodeableConcept feature-consequence
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" : "feature-consequence"
    }
  ]
}
Observation.Slices for component.component:feature-consequence.value[x] This element is included in summaries. 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence Value Set (extensible): Concepts in sequence ontology under SO:0001537.
Observation.Slices for component.component:functional-effect This element is included in summaries. 0..1 BackboneElement Functional Effect
Observation.Slices for component.component:functional-effect.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:functional-effect.code This element is included in summaries. 1..1 CodeableConcept functional-effect
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" : "functional-effect"
    }
  ]
}
Observation.Slices for component.component:functional-effect.value[x] This element is included in summaries. 1..1 CodeableConcept gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect Value Set (extensible): Sequence Ontology terms under SO:0001536

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:evidence-level.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:evidence-level.​value[x] Base example Evidence Level Examples 📦4.0.0-cibuild This IG
Observation.component:clinical-significance.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:clinical-significance.​value[x] Base example LOINC Answer Codes for LL4034-6 ∅ unknown?
Observation.component:knowledge-base.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:knowledge-base.​value[x] Base example Knowledge Base Version Codes 📦4.0.0-cibuild This IG
Observation.component:annotation-pipeline.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:transcript-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:protein-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:protein-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:feature-consequence.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:feature-consequence.​value[x] Base extensible Molecular Consequence Value Set 📦4.0.0-cibuild This IG
Observation.component:functional-effect.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:functional-effect.​value[x] Base extensible Functional Effect Value Set 📦4.0.0-cibuild This IG

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 GenomicImplication

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation 0..* GenomicImplication Molecular Consequence
Observation.code 1..1 CodeableConcept molecular-consequence
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "molecular-consequence"
    }
  ]
}
Observation.Slices for component Content/Rules for all slices
Observation.Slices for component.component:coding-hgvs 0..1 BackboneElement DNA change (c.HGVS)
Observation.Slices for component.component:coding-hgvs.code 1..1 CodeableConcept 48004-6
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48004-6"
    }
  ]
}
Observation.Slices for component.component:coding-hgvs.value[x] 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:transcript-ref-seq 0..1 BackboneElement Reference Transcript
Observation.Slices for component.component:transcript-ref-seq.code 1..1 CodeableConcept 51958-7
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51958-7"
    }
  ]
}
Observation.Slices for component.component:transcript-ref-seq.value[x] 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:protein-hgvs 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
Observation.Slices for component.component:protein-hgvs.code 1..1 CodeableConcept 48005-3
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48005-3"
    }
  ]
}
Observation.Slices for component.component:protein-hgvs.value[x] 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:protein-ref-seq 0..1 BackboneElement Protein Reference Sequence
Observation.Slices for component.component:protein-ref-seq.code 1..1 CodeableConcept protein-ref-seq
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "protein-ref-seq"
    }
  ]
}
Observation.Slices for component.component:protein-ref-seq.value[x] 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:feature-consequence 0..* BackboneElement Feature Consequence
Observation.Slices for component.component:feature-consequence.code 1..1 CodeableConcept feature-consequence
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "feature-consequence"
    }
  ]
}
Observation.Slices for component.component:feature-consequence.value[x] 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence Value Set (extensible): Concepts in sequence ontology under SO:0001537.
Observation.Slices for component.component:functional-effect 0..1 BackboneElement Functional Effect
Observation.Slices for component.component:functional-effect.code 1..1 CodeableConcept functional-effect
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "functional-effect"
    }
  ]
}
Observation.Slices for component.component:functional-effect.value[x] 1..1 CodeableConcept gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect Value Set (extensible): Sequence Ontology terms under SO:0001536

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:feature-consequence.​value[x] Base extensible Molecular Consequence Value Set 📦4.0.0-cibuild This IG
Observation.component:functional-effect.​value[x] Base extensible Functional Effect Value Set 📦4.0.0-cibuild This IG
NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicImplication Molecular Consequence
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.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
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 molecular-consequence
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" : "molecular-consequence"
    }
  ]
}
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.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.Slices for derivedFrom This element is included in summaries. 1..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
Observation.Slices for derivedFrom.derivedFrom:variant This element is included in summaries. 0..* Reference(Variant) Variant the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:genotype This element is included in summaries. 0..* Reference(Genotype) Genotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:haplotype This element is included in summaries. 0..* Reference(Haplotype) Haplotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:biomarker This element is included in summaries. 0..* Reference(Molecular Biomarker) MolecularBiomarker the implication is derived from
Observation.Slices for component This element is included in summaries. 0..* BackboneElement Component results
Slice: Unordered, Open by value:code

Slicing Note: The rules on this element (including its children) apply to all the slices, but are not repeated in them
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.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:All Slices.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
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:evidence-level This element is included in summaries. 0..* BackboneElement Level of Evidence
Observation.Slices for component.component:evidence-level.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:evidence-level.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:evidence-level.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:evidence-level.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:evidence-level.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:evidence-level.code This element is included in summaries. 1..1 CodeableConcept 93044-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "93044-6"
    }
  ]
}
Observation.Slices for component.component:evidence-level.value[x] This element is included in summaries. 1..1 CodeableConcept 1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star
Binding: Evidence Level Examples (example): PharmGKB or ClinVar
Observation.Slices for component.component:evidence-level.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:evidence-level.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:evidence-level.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:clinical-significance This element is included in summaries. 0..1 BackboneElement Clinical significance
Observation.Slices for component.component:clinical-significance.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:clinical-significance.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:clinical-significance.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:clinical-significance.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:clinical-significance.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:clinical-significance.code This element is included in summaries. 1..1 CodeableConcept 53037-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "53037-8"
    }
  ]
}
Observation.Slices for component.component:clinical-significance.value[x] This element is included in summaries. 1..1 CodeableConcept Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (example)
Observation.Slices for component.component:clinical-significance.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:clinical-significance.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:clinical-significance.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:knowledge-base This element is included in summaries. 0..1 BackboneElement Knowledge Base
Observation.Slices for component.component:knowledge-base.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:knowledge-base.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:knowledge-base.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:knowledge-base.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:knowledge-base.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:knowledge-base.code This element is included in summaries. 1..1 CodeableConcept knowledge-base
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" : "knowledge-base"
    }
  ]
}
Observation.Slices for component.component:knowledge-base.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Binding: Knowledge Base Version Codes (example)
Observation.Slices for component.component:knowledge-base.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:knowledge-base.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:knowledge-base.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:annotation-pipeline This element is included in summaries. 0..1 BackboneElement Annotation Pipeline
Observation.Slices for component.component:annotation-pipeline.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:annotation-pipeline.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:annotation-pipeline.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:annotation-pipeline.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:annotation-pipeline.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:annotation-pipeline.code This element is included in summaries. 1..1 CodeableConcept annotation-pipeline
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" : "annotation-pipeline"
    }
  ]
}
Observation.Slices for component.component:annotation-pipeline.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Observation.Slices for component.component:annotation-pipeline.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:annotation-pipeline.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:annotation-pipeline.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:coding-hgvs This element is included in summaries. 0..1 BackboneElement DNA change (c.HGVS)
Observation.Slices for component.component:coding-hgvs.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:coding-hgvs.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:coding-hgvs.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:coding-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48004-6"
    }
  ]
}
Observation.Slices for component.component:coding-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:coding-hgvs.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:coding-hgvs.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:coding-hgvs.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:transcript-ref-seq This element is included in summaries. 0..1 BackboneElement Reference Transcript
Observation.Slices for component.component:transcript-ref-seq.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:transcript-ref-seq.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:transcript-ref-seq.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:transcript-ref-seq.code This element is included in summaries. 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51958-7"
    }
  ]
}
Observation.Slices for component.component:transcript-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:transcript-ref-seq.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:transcript-ref-seq.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:transcript-ref-seq.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:protein-hgvs This element is included in summaries. 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
Observation.Slices for component.component:protein-hgvs.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:protein-hgvs.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:protein-hgvs.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:protein-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48005-3"
    }
  ]
}
Observation.Slices for component.component:protein-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:protein-hgvs.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:protein-hgvs.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:protein-hgvs.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:protein-ref-seq This element is included in summaries. 0..1 BackboneElement Protein Reference Sequence
Observation.Slices for component.component:protein-ref-seq.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:protein-ref-seq.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:protein-ref-seq.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:protein-ref-seq.code This element is included in summaries. 1..1 CodeableConcept protein-ref-seq
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" : "protein-ref-seq"
    }
  ]
}
Observation.Slices for component.component:protein-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:protein-ref-seq.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:protein-ref-seq.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:protein-ref-seq.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:feature-consequence This element is included in summaries. 0..* BackboneElement Feature Consequence
Observation.Slices for component.component:feature-consequence.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:feature-consequence.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:feature-consequence.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:feature-consequence.code This element is included in summaries. 1..1 CodeableConcept feature-consequence
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" : "feature-consequence"
    }
  ]
}
Observation.Slices for component.component:feature-consequence.value[x] This element is included in summaries. 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence Value Set (extensible): Concepts in sequence ontology under SO:0001537.
Observation.Slices for component.component:feature-consequence.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:feature-consequence.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:feature-consequence.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:functional-effect This element is included in summaries. 0..1 BackboneElement Functional Effect
Observation.Slices for component.component:functional-effect.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:functional-effect.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:functional-effect.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:functional-effect.code This element is included in summaries. 1..1 CodeableConcept functional-effect
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" : "functional-effect"
    }
  ]
}
Observation.Slices for component.component:functional-effect.value[x] This element is included in summaries. 1..1 CodeableConcept gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect Value Set (extensible): Sequence Ontology terms under SO:0001536
Observation.Slices for component.component:functional-effect.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:functional-effect.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:functional-effect.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:evidence-level.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:evidence-level.​value[x] Base example Evidence Level Examples 📦4.0.0-cibuild This IG
Observation.component:evidence-level.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:evidence-level.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:clinical-significance.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:clinical-significance.​value[x] Base example LOINC Answer Codes for LL4034-6 ∅ unknown?
Observation.component:clinical-significance.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:clinical-significance.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:knowledge-base.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:knowledge-base.​value[x] Base example Knowledge Base Version Codes 📦4.0.0-cibuild This IG
Observation.component:knowledge-base.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:knowledge-base.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:annotation-pipeline.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:annotation-pipeline.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:annotation-pipeline.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:coding-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:transcript-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:protein-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:protein-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:protein-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:protein-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:feature-consequence.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:feature-consequence.​value[x] Base extensible Molecular Consequence Value Set 📦4.0.0-cibuild This IG
Observation.component:feature-consequence.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:feature-consequence.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:functional-effect.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:functional-effect.​value[x] Base extensible Functional Effect Value Set 📦4.0.0-cibuild This IG
Observation.component:functional-effect.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:functional-effect.​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 GenomicImplication

Summary

Mandatory: 0 element(6 nested mandatory elements)

Maturity: 2

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicImplication Molecular Consequence
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.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
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 molecular-consequence
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" : "molecular-consequence"
    }
  ]
}
Observation.Slices for derivedFrom This element is included in summaries. 1..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
Observation.Slices for derivedFrom.derivedFrom:variant This element is included in summaries. 0..* Reference(Variant) Variant the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:genotype This element is included in summaries. 0..* Reference(Genotype) Genotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:haplotype This element is included in summaries. 0..* Reference(Haplotype) Haplotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:biomarker This element is included in summaries. 0..* Reference(Molecular Biomarker) MolecularBiomarker the implication is derived from
Observation.Slices for component This element is included in summaries. 0..* BackboneElement Component results
Slice: Unordered, Open by value:code

Slicing Note: The rules on this element (including its children) apply to all the slices, but are not repeated in them
Observation.Slices for component.component:All Slices Content/Rules for all slices
Observation.Slices for component.component:All Slices.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:All Slices.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
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:evidence-level This element is included in summaries. 0..* BackboneElement Level of Evidence
Observation.Slices for component.component:evidence-level.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:evidence-level.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:evidence-level.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:evidence-level.code This element is included in summaries. 1..1 CodeableConcept 93044-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "93044-6"
    }
  ]
}
Observation.Slices for component.component:evidence-level.value[x] This element is included in summaries. 1..1 CodeableConcept 1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star
Binding: Evidence Level Examples (example): PharmGKB or ClinVar
Observation.Slices for component.component:clinical-significance This element is included in summaries. 0..1 BackboneElement Clinical significance
Observation.Slices for component.component:clinical-significance.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:clinical-significance.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:clinical-significance.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:clinical-significance.code This element is included in summaries. 1..1 CodeableConcept 53037-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "53037-8"
    }
  ]
}
Observation.Slices for component.component:clinical-significance.value[x] This element is included in summaries. 1..1 CodeableConcept Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (example)
Observation.Slices for component.component:knowledge-base This element is included in summaries. 0..1 BackboneElement Knowledge Base
Observation.Slices for component.component:knowledge-base.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:knowledge-base.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:knowledge-base.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:knowledge-base.code This element is included in summaries. 1..1 CodeableConcept knowledge-base
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" : "knowledge-base"
    }
  ]
}
Observation.Slices for component.component:knowledge-base.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Binding: Knowledge Base Version Codes (example)
Observation.Slices for component.component:annotation-pipeline This element is included in summaries. 0..1 BackboneElement Annotation Pipeline
Observation.Slices for component.component:annotation-pipeline.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:annotation-pipeline.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:annotation-pipeline.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:annotation-pipeline.code This element is included in summaries. 1..1 CodeableConcept annotation-pipeline
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" : "annotation-pipeline"
    }
  ]
}
Observation.Slices for component.component:annotation-pipeline.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Observation.Slices for component.component:coding-hgvs This element is included in summaries. 0..1 BackboneElement DNA change (c.HGVS)
Observation.Slices for component.component:coding-hgvs.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:coding-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48004-6"
    }
  ]
}
Observation.Slices for component.component:coding-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:transcript-ref-seq This element is included in summaries. 0..1 BackboneElement Reference Transcript
Observation.Slices for component.component:transcript-ref-seq.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:transcript-ref-seq.code This element is included in summaries. 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51958-7"
    }
  ]
}
Observation.Slices for component.component:transcript-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:protein-hgvs This element is included in summaries. 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
Observation.Slices for component.component:protein-hgvs.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:protein-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48005-3"
    }
  ]
}
Observation.Slices for component.component:protein-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:protein-ref-seq This element is included in summaries. 0..1 BackboneElement Protein Reference Sequence
Observation.Slices for component.component:protein-ref-seq.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:protein-ref-seq.code This element is included in summaries. 1..1 CodeableConcept protein-ref-seq
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" : "protein-ref-seq"
    }
  ]
}
Observation.Slices for component.component:protein-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:feature-consequence This element is included in summaries. 0..* BackboneElement Feature Consequence
Observation.Slices for component.component:feature-consequence.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:feature-consequence.code This element is included in summaries. 1..1 CodeableConcept feature-consequence
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" : "feature-consequence"
    }
  ]
}
Observation.Slices for component.component:feature-consequence.value[x] This element is included in summaries. 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence Value Set (extensible): Concepts in sequence ontology under SO:0001537.
Observation.Slices for component.component:functional-effect This element is included in summaries. 0..1 BackboneElement Functional Effect
Observation.Slices for component.component:functional-effect.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:functional-effect.code This element is included in summaries. 1..1 CodeableConcept functional-effect
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" : "functional-effect"
    }
  ]
}
Observation.Slices for component.component:functional-effect.value[x] This element is included in summaries. 1..1 CodeableConcept gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect Value Set (extensible): Sequence Ontology terms under SO:0001536

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:evidence-level.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:evidence-level.​value[x] Base example Evidence Level Examples 📦4.0.0-cibuild This IG
Observation.component:clinical-significance.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:clinical-significance.​value[x] Base example LOINC Answer Codes for LL4034-6 ∅ unknown?
Observation.component:knowledge-base.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:knowledge-base.​value[x] Base example Knowledge Base Version Codes 📦4.0.0-cibuild This IG
Observation.component:annotation-pipeline.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:transcript-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:protein-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:protein-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:feature-consequence.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:feature-consequence.​value[x] Base extensible Molecular Consequence Value Set 📦4.0.0-cibuild This IG
Observation.component:functional-effect.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:functional-effect.​value[x] Base extensible Functional Effect Value Set 📦4.0.0-cibuild This IG

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 GenomicImplication

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation 0..* GenomicImplication Molecular Consequence
Observation.code 1..1 CodeableConcept molecular-consequence
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "molecular-consequence"
    }
  ]
}
Observation.Slices for component Content/Rules for all slices
Observation.Slices for component.component:coding-hgvs 0..1 BackboneElement DNA change (c.HGVS)
Observation.Slices for component.component:coding-hgvs.code 1..1 CodeableConcept 48004-6
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48004-6"
    }
  ]
}
Observation.Slices for component.component:coding-hgvs.value[x] 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:transcript-ref-seq 0..1 BackboneElement Reference Transcript
Observation.Slices for component.component:transcript-ref-seq.code 1..1 CodeableConcept 51958-7
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51958-7"
    }
  ]
}
Observation.Slices for component.component:transcript-ref-seq.value[x] 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:protein-hgvs 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
Observation.Slices for component.component:protein-hgvs.code 1..1 CodeableConcept 48005-3
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48005-3"
    }
  ]
}
Observation.Slices for component.component:protein-hgvs.value[x] 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:protein-ref-seq 0..1 BackboneElement Protein Reference Sequence
Observation.Slices for component.component:protein-ref-seq.code 1..1 CodeableConcept protein-ref-seq
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "protein-ref-seq"
    }
  ]
}
Observation.Slices for component.component:protein-ref-seq.value[x] 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:feature-consequence 0..* BackboneElement Feature Consequence
Observation.Slices for component.component:feature-consequence.code 1..1 CodeableConcept feature-consequence
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "feature-consequence"
    }
  ]
}
Observation.Slices for component.component:feature-consequence.value[x] 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence Value Set (extensible): Concepts in sequence ontology under SO:0001537.
Observation.Slices for component.component:functional-effect 0..1 BackboneElement Functional Effect
Observation.Slices for component.component:functional-effect.code 1..1 CodeableConcept functional-effect
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "functional-effect"
    }
  ]
}
Observation.Slices for component.component:functional-effect.value[x] 1..1 CodeableConcept gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect Value Set (extensible): Sequence Ontology terms under SO:0001536

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:feature-consequence.​value[x] Base extensible Molecular Consequence Value Set 📦4.0.0-cibuild This IG
Observation.component:functional-effect.​value[x] Base extensible Functional Effect Value Set 📦4.0.0-cibuild This IG

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicImplication Molecular Consequence
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.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
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 molecular-consequence
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" : "molecular-consequence"
    }
  ]
}
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.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.Slices for derivedFrom This element is included in summaries. 1..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
Observation.Slices for derivedFrom.derivedFrom:variant This element is included in summaries. 0..* Reference(Variant) Variant the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:genotype This element is included in summaries. 0..* Reference(Genotype) Genotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:haplotype This element is included in summaries. 0..* Reference(Haplotype) Haplotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:biomarker This element is included in summaries. 0..* Reference(Molecular Biomarker) MolecularBiomarker the implication is derived from
Observation.Slices for component This element is included in summaries. 0..* BackboneElement Component results
Slice: Unordered, Open by value:code

Slicing Note: The rules on this element (including its children) apply to all the slices, but are not repeated in them
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.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:All Slices.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
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:evidence-level This element is included in summaries. 0..* BackboneElement Level of Evidence
Observation.Slices for component.component:evidence-level.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:evidence-level.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:evidence-level.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:evidence-level.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:evidence-level.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:evidence-level.code This element is included in summaries. 1..1 CodeableConcept 93044-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "93044-6"
    }
  ]
}
Observation.Slices for component.component:evidence-level.value[x] This element is included in summaries. 1..1 CodeableConcept 1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star
Binding: Evidence Level Examples (example): PharmGKB or ClinVar
Observation.Slices for component.component:evidence-level.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:evidence-level.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:evidence-level.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:clinical-significance This element is included in summaries. 0..1 BackboneElement Clinical significance
Observation.Slices for component.component:clinical-significance.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:clinical-significance.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:clinical-significance.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:clinical-significance.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:clinical-significance.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:clinical-significance.code This element is included in summaries. 1..1 CodeableConcept 53037-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "53037-8"
    }
  ]
}
Observation.Slices for component.component:clinical-significance.value[x] This element is included in summaries. 1..1 CodeableConcept Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (example)
Observation.Slices for component.component:clinical-significance.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:clinical-significance.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:clinical-significance.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:knowledge-base This element is included in summaries. 0..1 BackboneElement Knowledge Base
Observation.Slices for component.component:knowledge-base.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:knowledge-base.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:knowledge-base.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:knowledge-base.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:knowledge-base.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:knowledge-base.code This element is included in summaries. 1..1 CodeableConcept knowledge-base
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" : "knowledge-base"
    }
  ]
}
Observation.Slices for component.component:knowledge-base.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Binding: Knowledge Base Version Codes (example)
Observation.Slices for component.component:knowledge-base.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:knowledge-base.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:knowledge-base.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:annotation-pipeline This element is included in summaries. 0..1 BackboneElement Annotation Pipeline
Observation.Slices for component.component:annotation-pipeline.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:annotation-pipeline.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:annotation-pipeline.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:annotation-pipeline.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:annotation-pipeline.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:annotation-pipeline.code This element is included in summaries. 1..1 CodeableConcept annotation-pipeline
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" : "annotation-pipeline"
    }
  ]
}
Observation.Slices for component.component:annotation-pipeline.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Observation.Slices for component.component:annotation-pipeline.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:annotation-pipeline.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:annotation-pipeline.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:coding-hgvs This element is included in summaries. 0..1 BackboneElement DNA change (c.HGVS)
Observation.Slices for component.component:coding-hgvs.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:coding-hgvs.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:coding-hgvs.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:coding-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48004-6"
    }
  ]
}
Observation.Slices for component.component:coding-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:coding-hgvs.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:coding-hgvs.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:coding-hgvs.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:transcript-ref-seq This element is included in summaries. 0..1 BackboneElement Reference Transcript
Observation.Slices for component.component:transcript-ref-seq.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:transcript-ref-seq.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:transcript-ref-seq.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:transcript-ref-seq.code This element is included in summaries. 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51958-7"
    }
  ]
}
Observation.Slices for component.component:transcript-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:transcript-ref-seq.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:transcript-ref-seq.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:transcript-ref-seq.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:protein-hgvs This element is included in summaries. 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
Observation.Slices for component.component:protein-hgvs.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:protein-hgvs.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:protein-hgvs.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:protein-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48005-3"
    }
  ]
}
Observation.Slices for component.component:protein-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:protein-hgvs.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:protein-hgvs.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:protein-hgvs.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:protein-ref-seq This element is included in summaries. 0..1 BackboneElement Protein Reference Sequence
Observation.Slices for component.component:protein-ref-seq.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:protein-ref-seq.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:protein-ref-seq.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:protein-ref-seq.code This element is included in summaries. 1..1 CodeableConcept protein-ref-seq
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" : "protein-ref-seq"
    }
  ]
}
Observation.Slices for component.component:protein-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:protein-ref-seq.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:protein-ref-seq.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:protein-ref-seq.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:feature-consequence This element is included in summaries. 0..* BackboneElement Feature Consequence
Observation.Slices for component.component:feature-consequence.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:feature-consequence.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:feature-consequence.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:feature-consequence.code This element is included in summaries. 1..1 CodeableConcept feature-consequence
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" : "feature-consequence"
    }
  ]
}
Observation.Slices for component.component:feature-consequence.value[x] This element is included in summaries. 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence Value Set (extensible): Concepts in sequence ontology under SO:0001537.
Observation.Slices for component.component:feature-consequence.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:feature-consequence.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:feature-consequence.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:functional-effect This element is included in summaries. 0..1 BackboneElement Functional Effect
Observation.Slices for component.component:functional-effect.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:functional-effect.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:functional-effect.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:functional-effect.code This element is included in summaries. 1..1 CodeableConcept functional-effect
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" : "functional-effect"
    }
  ]
}
Observation.Slices for component.component:functional-effect.value[x] This element is included in summaries. 1..1 CodeableConcept gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect Value Set (extensible): Sequence Ontology terms under SO:0001536
Observation.Slices for component.component:functional-effect.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:functional-effect.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:functional-effect.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:evidence-level.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:evidence-level.​value[x] Base example Evidence Level Examples 📦4.0.0-cibuild This IG
Observation.component:evidence-level.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:evidence-level.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:clinical-significance.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:clinical-significance.​value[x] Base example LOINC Answer Codes for LL4034-6 ∅ unknown?
Observation.component:clinical-significance.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:clinical-significance.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:knowledge-base.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:knowledge-base.​value[x] Base example Knowledge Base Version Codes 📦4.0.0-cibuild This IG
Observation.component:knowledge-base.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:knowledge-base.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:annotation-pipeline.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:annotation-pipeline.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:annotation-pipeline.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:coding-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:transcript-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:protein-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:protein-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:protein-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:protein-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:feature-consequence.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:feature-consequence.​value[x] Base extensible Molecular Consequence Value Set 📦4.0.0-cibuild This IG
Observation.component:feature-consequence.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:feature-consequence.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:functional-effect.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:functional-effect.​value[x] Base extensible Functional Effect Value Set 📦4.0.0-cibuild This IG
Observation.component:functional-effect.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:functional-effect.​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 GenomicImplication

Summary

Mandatory: 0 element(6 nested mandatory elements)

Maturity: 2

 

Other representations of profile: CSV, Excel, Schematron