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: Therapeutic Implication

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

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.

Observation stating a therapeutic annotation (e.g. drug susceptibility, clinical trial eligibility) on one or more genotype/haplotype/variant/biomarker observations.

This section provides guidance for genomic reporting about the implication of a patient's genetics on the behavior of one or more medications or other therapeutic alternatives (such as clinical trials).

This portion of the implementation guide relies on the content in the General Genomic Reporting and Variant Reporting portions of this implementation guide. Pharmacogenomic reports supplement this information with a set of pharmacogenomic-specific implication profiles. Implementers of pharmacogenomic reporting may also be interested in the Somatic Reporting section of this implementation guide.

Communicating disease or tumor context

In general, treatments and medications have a set of indications for use which are not explicitly stated. However, if a pharmacogenomics statement has a specific context of a disease or a tumor use the component phenotypic-treatment-context to indicate the disease.

Pharmacogenomic-specific Genomic Implications

Diagram showing the 3 medication implication profiles and the associated Medication Recommendation task

Figure 1: Pharmacogenomic Implications

(Profile links: Genomic Implication, Therapeutic Implication, Medication Recommendadtion)

There are two ways to communicate details about a medication whose implication is being described. The profile component medication-assessed is the place to communicate a simple code for the medication. If more detail about the medication is to be shared, use the extension named medication-assessed-reference. The extension can refer to a Medication or MedicationKnowledge resource. This might be used to share specific classification details if they are important as part of the implication being described. It is important to note that since there two ways to do this, implementers SHALL ensure consistent usage. If both the extension and component are used at the same time, they SHALL deliver the same medication. Because this is an international profile, no guidance is provided on drug coding systems.

It is important to note there are also two ways to communicate details about non-medication therapies (e.g. altered diet, radiation therapy, surgery, etc.). The profile component therapy-assessed is the place to communicate a simple code for the therapy. If more detail about the therapy is to be shared, use the extension named therapy-assessed-reference. The extension can refer to a CarePlan, ResearchStudy, or PlanDefinition resource. It is important to note that since there two ways to do this, implementers SHALL ensure consistent usage. If both the extension and component are used at the same time, they SHALL deliver the same therapy. Because this is an international profile, no guidance is provided on therapy coding systems.

The component therapeutic-implication lists one or more ramifications based on the presence of associated molecular finding(s), which may include:

  • Alterations in drug metabolism (or pharmacokinetics) that determine the concentration of the drug, prodrug, and/or break-down products over time;
  • Alterations in drug efficacy (or pharmacodynamics) that determine how effective a drug is at a given concentration;
  • Alterations that alter the risk of adverse drug events, or other types of implications that indicate altered responsiveness to other types of therapies or eligibility for clinical trials;
  • Other pharmacogenomic statements as necessary, by extending the valueSet.

To associate a therapeutic implication instance with a recommendation (e.g. discontinuing a medication, altering dosage, choose alternative medication) use Medication Recommendation, Followup Recommendation, along with current medication if appropriate. Use the Related Artifact extension for supporting documents such as CPIC guidelines.

Medication Recommendation tasks link to therapeutic implications through reasonReference and are included in the report using the recommended-action extension. The therapeutic implications do not have a link to medication recommendations, so the revinclude search parameter can be used to find the therapeutic implication statements relevant to the recommendations.

Note: If multiple medications are used in medication assessed, the usage implication should describe the combined effect.

Note 2: Implementers may also be interested in the Somatic Reporting and Pharmacogenomics Reporting sections of this implementation guide.

evidence-level versus clinical-significance

See Genomic Implication for guidance.

Differentiating AND vs OR

See Genomic Implication for guidance. Implication fields affected by this guidance include: derivedFrom, evidence-level, therapeutic-implication, phenotypic-treatment-context, medication-assessed, therapy-assessed.

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 Therapeutic Implication
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 therapeutic-implication
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" : "therapeutic-implication"
    }
  ]
}
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:therapeutic-implication This element is included in summaries. 0..* BackboneElement Therapeutic Implication
Observation.Slices for component.component:therapeutic-implication.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:therapeutic-implication.code This element is included in summaries. 1..1 CodeableConcept therapeutic-implication
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" : "therapeutic-implication"
    }
  ]
}
Observation.Slices for component.component:therapeutic-implication.value[x] This element is included in summaries. 1..1 CodeableConcept Responsive | Resistant | Poor metabolizer | Rapid metabolizer | Decreased function | Increased function | Does not meet eligibility criteria for clinical trial | ... (more)
Binding: Genetic Therapeutic Implications (extensible)
Observation.Slices for component.component:phenotypic-treatment-context This element is included in summaries. 0..* BackboneElement Phenotypic treatment context
Observation.Slices for component.component:phenotypic-treatment-context.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:phenotypic-treatment-context.code This element is included in summaries. 1..1 CodeableConcept 81259-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81259-4"
    }
  ]
}
Observation.Slices for component.component:phenotypic-treatment-context.value[x] This element is included in summaries. 1..1 CodeableConcept Contextual phenotype/condition code
Binding Description: (example): Binding not yet defined (examples: SNOMED CT Clinical findings, ICD-10-CM chapters 1-18, HPO terms)
Observation.Slices for component.component:medication-assessed This element is included in summaries. 0..* BackboneElement Medication Assessed
Observation.Slices for component.component:medication-assessed.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:medication-assessed.Slices for extension.extension:medication-assessed-reference 0..* Reference(Medication | MedicationKnowledge) Medication Assessed reference to a FHIR resource
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-assessed-reference
Observation.Slices for component.component:medication-assessed.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:medication-assessed.code This element is included in summaries. 1..1 CodeableConcept 51963-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51963-7"
    }
  ]
}
Observation.Slices for component.component:medication-assessed.value[x] This element is included in summaries. 1..1 CodeableConcept Medication code
Binding Description: (example): Binding not yet defined (RxNorm or similar)
Observation.Slices for component.component:therapy-assessed This element is included in summaries. 0..* BackboneElement Non-medication therapy assessed
Observation.Slices for component.component:therapy-assessed.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:therapy-assessed.Slices for extension.extension:therapy-assessed-reference 0..* Reference(CarePlan | ResearchStudy | PlanDefinition) Therapy Assessed reference to a FHIR resource
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapy-assessed-reference
Observation.Slices for component.component:therapy-assessed.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:therapy-assessed.code This element is included in summaries. 1..1 CodeableConcept associated-therapy
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" : "associated-therapy"
    }
  ]
}
Observation.Slices for component.component:therapy-assessed.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined

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:therapeutic-implication.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:therapeutic-implication.​value[x] Base extensible Genetic Therapeutic Implications 📦4.0.0-cibuild This IG
Observation.component:phenotypic-treatment-context.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:phenotypic-treatment-context.​value[x] Base example Not State Unknown
Observation.component:medication-assessed.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:medication-assessed.​value[x] Base example Not State Unknown
Observation.component:therapy-assessed.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:therapy-assessed.​value[x] Base example Not State Unknown

Constraints

Id Grade Path(s) Description Expression
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from GenomicImplication

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation 0..* GenomicImplication Therapeutic Implication
Observation.code 1..1 CodeableConcept therapeutic-implication
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "therapeutic-implication"
    }
  ]
}
Observation.Slices for component Content/Rules for all slices
Observation.Slices for component.component:therapeutic-implication 0..* BackboneElement Therapeutic Implication
Observation.Slices for component.component:therapeutic-implication.code 1..1 CodeableConcept therapeutic-implication
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "therapeutic-implication"
    }
  ]
}
Observation.Slices for component.component:therapeutic-implication.value[x] 1..1 CodeableConcept Responsive | Resistant | Poor metabolizer | Rapid metabolizer | Decreased function | Increased function | Does not meet eligibility criteria for clinical trial | ... (more)
Binding: Genetic Therapeutic Implications (extensible)
Observation.Slices for component.component:phenotypic-treatment-context 0..* BackboneElement Phenotypic treatment context
Observation.Slices for component.component:phenotypic-treatment-context.code 1..1 CodeableConcept 81259-4
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81259-4"
    }
  ]
}
Observation.Slices for component.component:phenotypic-treatment-context.value[x] 1..1 CodeableConcept Contextual phenotype/condition code
Binding Description: (example): Binding not yet defined (examples: SNOMED CT Clinical findings, ICD-10-CM chapters 1-18, HPO terms)
Observation.Slices for component.component:medication-assessed 0..* BackboneElement Medication Assessed
Observation.Slices for component.component:medication-assessed.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:medication-assessed.Slices for extension.extension:medication-assessed-reference 0..* Reference(Medication | MedicationKnowledge) Medication Assessed reference to a FHIR resource
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-assessed-reference
Observation.Slices for component.component:medication-assessed.code 1..1 CodeableConcept 51963-7
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51963-7"
    }
  ]
}
Observation.Slices for component.component:medication-assessed.value[x] 1..1 CodeableConcept Medication code
Binding Description: (example): Binding not yet defined (RxNorm or similar)
Observation.Slices for component.component:therapy-assessed 0..* BackboneElement Non-medication therapy assessed
Observation.Slices for component.component:therapy-assessed.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:therapy-assessed.Slices for extension.extension:therapy-assessed-reference 0..* Reference(CarePlan | ResearchStudy | PlanDefinition) Therapy Assessed reference to a FHIR resource
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapy-assessed-reference
Observation.Slices for component.component:therapy-assessed.code 1..1 CodeableConcept associated-therapy
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "associated-therapy"
    }
  ]
}
Observation.Slices for component.component:therapy-assessed.value[x] 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Observation.component:therapeutic-implication.​value[x] Base extensible Genetic Therapeutic Implications 📦4.0.0-cibuild This IG
Observation.component:phenotypic-treatment-context.​value[x] Base example Not State Unknown
Observation.component:medication-assessed.​value[x] Base example Not State Unknown
Observation.component:therapy-assessed.​value[x] Base example Not State Unknown
NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicImplication Therapeutic Implication
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 therapeutic-implication
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" : "therapeutic-implication"
    }
  ]
}
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:therapeutic-implication This element is included in summaries. 0..* BackboneElement Therapeutic Implication
Observation.Slices for component.component:therapeutic-implication.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:therapeutic-implication.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:therapeutic-implication.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:therapeutic-implication.code This element is included in summaries. 1..1 CodeableConcept therapeutic-implication
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" : "therapeutic-implication"
    }
  ]
}
Observation.Slices for component.component:therapeutic-implication.value[x] This element is included in summaries. 1..1 CodeableConcept Responsive | Resistant | Poor metabolizer | Rapid metabolizer | Decreased function | Increased function | Does not meet eligibility criteria for clinical trial | ... (more)
Binding: Genetic Therapeutic Implications (extensible)
Observation.Slices for component.component:therapeutic-implication.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:therapeutic-implication.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:therapeutic-implication.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:phenotypic-treatment-context This element is included in summaries. 0..* BackboneElement Phenotypic treatment context
Observation.Slices for component.component:phenotypic-treatment-context.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:phenotypic-treatment-context.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:phenotypic-treatment-context.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:phenotypic-treatment-context.code This element is included in summaries. 1..1 CodeableConcept 81259-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81259-4"
    }
  ]
}
Observation.Slices for component.component:phenotypic-treatment-context.value[x] This element is included in summaries. 1..1 CodeableConcept Contextual phenotype/condition code
Binding Description: (example): Binding not yet defined (examples: SNOMED CT Clinical findings, ICD-10-CM chapters 1-18, HPO terms)
Observation.Slices for component.component:phenotypic-treatment-context.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:phenotypic-treatment-context.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:phenotypic-treatment-context.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:medication-assessed This element is included in summaries. 0..* BackboneElement Medication Assessed
Observation.Slices for component.component:medication-assessed.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:medication-assessed.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:medication-assessed.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:medication-assessed.Slices for extension.extension:medication-assessed-reference 0..* Reference(Medication | MedicationKnowledge) Medication Assessed reference to a FHIR resource
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-assessed-reference
Observation.Slices for component.component:medication-assessed.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:medication-assessed.code This element is included in summaries. 1..1 CodeableConcept 51963-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51963-7"
    }
  ]
}
Observation.Slices for component.component:medication-assessed.value[x] This element is included in summaries. 1..1 CodeableConcept Medication code
Binding Description: (example): Binding not yet defined (RxNorm or similar)
Observation.Slices for component.component:medication-assessed.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:medication-assessed.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:medication-assessed.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:therapy-assessed This element is included in summaries. 0..* BackboneElement Non-medication therapy assessed
Observation.Slices for component.component:therapy-assessed.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:therapy-assessed.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:therapy-assessed.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:therapy-assessed.Slices for extension.extension:therapy-assessed-reference 0..* Reference(CarePlan | ResearchStudy | PlanDefinition) Therapy Assessed reference to a FHIR resource
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapy-assessed-reference
Observation.Slices for component.component:therapy-assessed.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:therapy-assessed.code This element is included in summaries. 1..1 CodeableConcept associated-therapy
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" : "associated-therapy"
    }
  ]
}
Observation.Slices for component.component:therapy-assessed.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
Observation.Slices for component.component:therapy-assessed.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:therapy-assessed.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:therapy-assessed.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:therapeutic-implication.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:therapeutic-implication.​value[x] Base extensible Genetic Therapeutic Implications 📦4.0.0-cibuild This IG
Observation.component:therapeutic-implication.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:therapeutic-implication.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:phenotypic-treatment-context.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:phenotypic-treatment-context.​value[x] Base example Not State Unknown
Observation.component:phenotypic-treatment-context.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:phenotypic-treatment-context.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:medication-assessed.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:medication-assessed.​value[x] Base example Not State Unknown
Observation.component:medication-assessed.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:medication-assessed.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:therapy-assessed.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:therapy-assessed.​value[x] Base example Not State Unknown
Observation.component:therapy-assessed.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:therapy-assessed.​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

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicImplication Therapeutic Implication
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 therapeutic-implication
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" : "therapeutic-implication"
    }
  ]
}
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:therapeutic-implication This element is included in summaries. 0..* BackboneElement Therapeutic Implication
Observation.Slices for component.component:therapeutic-implication.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:therapeutic-implication.code This element is included in summaries. 1..1 CodeableConcept therapeutic-implication
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" : "therapeutic-implication"
    }
  ]
}
Observation.Slices for component.component:therapeutic-implication.value[x] This element is included in summaries. 1..1 CodeableConcept Responsive | Resistant | Poor metabolizer | Rapid metabolizer | Decreased function | Increased function | Does not meet eligibility criteria for clinical trial | ... (more)
Binding: Genetic Therapeutic Implications (extensible)
Observation.Slices for component.component:phenotypic-treatment-context This element is included in summaries. 0..* BackboneElement Phenotypic treatment context
Observation.Slices for component.component:phenotypic-treatment-context.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:phenotypic-treatment-context.code This element is included in summaries. 1..1 CodeableConcept 81259-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81259-4"
    }
  ]
}
Observation.Slices for component.component:phenotypic-treatment-context.value[x] This element is included in summaries. 1..1 CodeableConcept Contextual phenotype/condition code
Binding Description: (example): Binding not yet defined (examples: SNOMED CT Clinical findings, ICD-10-CM chapters 1-18, HPO terms)
Observation.Slices for component.component:medication-assessed This element is included in summaries. 0..* BackboneElement Medication Assessed
Observation.Slices for component.component:medication-assessed.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:medication-assessed.Slices for extension.extension:medication-assessed-reference 0..* Reference(Medication | MedicationKnowledge) Medication Assessed reference to a FHIR resource
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-assessed-reference
Observation.Slices for component.component:medication-assessed.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:medication-assessed.code This element is included in summaries. 1..1 CodeableConcept 51963-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51963-7"
    }
  ]
}
Observation.Slices for component.component:medication-assessed.value[x] This element is included in summaries. 1..1 CodeableConcept Medication code
Binding Description: (example): Binding not yet defined (RxNorm or similar)
Observation.Slices for component.component:therapy-assessed This element is included in summaries. 0..* BackboneElement Non-medication therapy assessed
Observation.Slices for component.component:therapy-assessed.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:therapy-assessed.Slices for extension.extension:therapy-assessed-reference 0..* Reference(CarePlan | ResearchStudy | PlanDefinition) Therapy Assessed reference to a FHIR resource
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapy-assessed-reference
Observation.Slices for component.component:therapy-assessed.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:therapy-assessed.code This element is included in summaries. 1..1 CodeableConcept associated-therapy
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" : "associated-therapy"
    }
  ]
}
Observation.Slices for component.component:therapy-assessed.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined

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:therapeutic-implication.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:therapeutic-implication.​value[x] Base extensible Genetic Therapeutic Implications 📦4.0.0-cibuild This IG
Observation.component:phenotypic-treatment-context.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:phenotypic-treatment-context.​value[x] Base example Not State Unknown
Observation.component:medication-assessed.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:medication-assessed.​value[x] Base example Not State Unknown
Observation.component:therapy-assessed.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:therapy-assessed.​value[x] Base example Not State Unknown

Constraints

Id Grade Path(s) Description Expression
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

Differential View

This structure is derived from GenomicImplication

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation 0..* GenomicImplication Therapeutic Implication
Observation.code 1..1 CodeableConcept therapeutic-implication
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "therapeutic-implication"
    }
  ]
}
Observation.Slices for component Content/Rules for all slices
Observation.Slices for component.component:therapeutic-implication 0..* BackboneElement Therapeutic Implication
Observation.Slices for component.component:therapeutic-implication.code 1..1 CodeableConcept therapeutic-implication
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "therapeutic-implication"
    }
  ]
}
Observation.Slices for component.component:therapeutic-implication.value[x] 1..1 CodeableConcept Responsive | Resistant | Poor metabolizer | Rapid metabolizer | Decreased function | Increased function | Does not meet eligibility criteria for clinical trial | ... (more)
Binding: Genetic Therapeutic Implications (extensible)
Observation.Slices for component.component:phenotypic-treatment-context 0..* BackboneElement Phenotypic treatment context
Observation.Slices for component.component:phenotypic-treatment-context.code 1..1 CodeableConcept 81259-4
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81259-4"
    }
  ]
}
Observation.Slices for component.component:phenotypic-treatment-context.value[x] 1..1 CodeableConcept Contextual phenotype/condition code
Binding Description: (example): Binding not yet defined (examples: SNOMED CT Clinical findings, ICD-10-CM chapters 1-18, HPO terms)
Observation.Slices for component.component:medication-assessed 0..* BackboneElement Medication Assessed
Observation.Slices for component.component:medication-assessed.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:medication-assessed.Slices for extension.extension:medication-assessed-reference 0..* Reference(Medication | MedicationKnowledge) Medication Assessed reference to a FHIR resource
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-assessed-reference
Observation.Slices for component.component:medication-assessed.code 1..1 CodeableConcept 51963-7
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51963-7"
    }
  ]
}
Observation.Slices for component.component:medication-assessed.value[x] 1..1 CodeableConcept Medication code
Binding Description: (example): Binding not yet defined (RxNorm or similar)
Observation.Slices for component.component:therapy-assessed 0..* BackboneElement Non-medication therapy assessed
Observation.Slices for component.component:therapy-assessed.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:therapy-assessed.Slices for extension.extension:therapy-assessed-reference 0..* Reference(CarePlan | ResearchStudy | PlanDefinition) Therapy Assessed reference to a FHIR resource
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapy-assessed-reference
Observation.Slices for component.component:therapy-assessed.code 1..1 CodeableConcept associated-therapy
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "associated-therapy"
    }
  ]
}
Observation.Slices for component.component:therapy-assessed.value[x] 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Observation.component:therapeutic-implication.​value[x] Base extensible Genetic Therapeutic Implications 📦4.0.0-cibuild This IG
Observation.component:phenotypic-treatment-context.​value[x] Base example Not State Unknown
Observation.component:medication-assessed.​value[x] Base example Not State Unknown
Observation.component:therapy-assessed.​value[x] Base example Not State Unknown

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicImplication Therapeutic Implication
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 therapeutic-implication
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" : "therapeutic-implication"
    }
  ]
}
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:therapeutic-implication This element is included in summaries. 0..* BackboneElement Therapeutic Implication
Observation.Slices for component.component:therapeutic-implication.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:therapeutic-implication.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:therapeutic-implication.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:therapeutic-implication.code This element is included in summaries. 1..1 CodeableConcept therapeutic-implication
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" : "therapeutic-implication"
    }
  ]
}
Observation.Slices for component.component:therapeutic-implication.value[x] This element is included in summaries. 1..1 CodeableConcept Responsive | Resistant | Poor metabolizer | Rapid metabolizer | Decreased function | Increased function | Does not meet eligibility criteria for clinical trial | ... (more)
Binding: Genetic Therapeutic Implications (extensible)
Observation.Slices for component.component:therapeutic-implication.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:therapeutic-implication.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:therapeutic-implication.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:phenotypic-treatment-context This element is included in summaries. 0..* BackboneElement Phenotypic treatment context
Observation.Slices for component.component:phenotypic-treatment-context.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:phenotypic-treatment-context.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:phenotypic-treatment-context.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:phenotypic-treatment-context.code This element is included in summaries. 1..1 CodeableConcept 81259-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81259-4"
    }
  ]
}
Observation.Slices for component.component:phenotypic-treatment-context.value[x] This element is included in summaries. 1..1 CodeableConcept Contextual phenotype/condition code
Binding Description: (example): Binding not yet defined (examples: SNOMED CT Clinical findings, ICD-10-CM chapters 1-18, HPO terms)
Observation.Slices for component.component:phenotypic-treatment-context.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:phenotypic-treatment-context.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:phenotypic-treatment-context.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:medication-assessed This element is included in summaries. 0..* BackboneElement Medication Assessed
Observation.Slices for component.component:medication-assessed.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:medication-assessed.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:medication-assessed.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:medication-assessed.Slices for extension.extension:medication-assessed-reference 0..* Reference(Medication | MedicationKnowledge) Medication Assessed reference to a FHIR resource
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-assessed-reference
Observation.Slices for component.component:medication-assessed.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:medication-assessed.code This element is included in summaries. 1..1 CodeableConcept 51963-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51963-7"
    }
  ]
}
Observation.Slices for component.component:medication-assessed.value[x] This element is included in summaries. 1..1 CodeableConcept Medication code
Binding Description: (example): Binding not yet defined (RxNorm or similar)
Observation.Slices for component.component:medication-assessed.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:medication-assessed.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:medication-assessed.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:therapy-assessed This element is included in summaries. 0..* BackboneElement Non-medication therapy assessed
Observation.Slices for component.component:therapy-assessed.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:therapy-assessed.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:therapy-assessed.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:therapy-assessed.Slices for extension.extension:therapy-assessed-reference 0..* Reference(CarePlan | ResearchStudy | PlanDefinition) Therapy Assessed reference to a FHIR resource
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapy-assessed-reference
Observation.Slices for component.component:therapy-assessed.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:therapy-assessed.code This element is included in summaries. 1..1 CodeableConcept associated-therapy
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" : "associated-therapy"
    }
  ]
}
Observation.Slices for component.component:therapy-assessed.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
Observation.Slices for component.component:therapy-assessed.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:therapy-assessed.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:therapy-assessed.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:therapeutic-implication.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:therapeutic-implication.​value[x] Base extensible Genetic Therapeutic Implications 📦4.0.0-cibuild This IG
Observation.component:therapeutic-implication.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:therapeutic-implication.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:phenotypic-treatment-context.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:phenotypic-treatment-context.​value[x] Base example Not State Unknown
Observation.component:phenotypic-treatment-context.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:phenotypic-treatment-context.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:medication-assessed.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:medication-assessed.​value[x] Base example Not State Unknown
Observation.component:medication-assessed.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:medication-assessed.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:therapy-assessed.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:therapy-assessed.​value[x] Base example Not State Unknown
Observation.component:therapy-assessed.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:therapy-assessed.​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

 

Other representations of profile: CSV, Excel, Schematron