Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot 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 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

Resource Profile: Molecular Consequence

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence Version: 3.0.1-SNAPSHOT
Active as of 2024-07-15 Computable Name: MolecularConsequence

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

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

Molecular Consequence Use Case

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

Detailed Example

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

Multiple transcripts of ODF2L gene

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

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

These following examples correspond to the annotated VCF row.

evidence-level versus clinical-significance

See Genomic Implication for guidance.

Differentiating AND vs OR

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

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

Usage:

Formal Views of Profile Content

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

This structure is derived from GenomicImplication

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..* GenomicImplication Molecular Consequence
... code 1..1 CodeableConcept molecular-consequence
Required Pattern: At least the following
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: molecular-consequence
... Slices for component Content/Rules for all slices
.... component:coding-hgvs 0..1 BackboneElement DNA change (c.HGVS)
..... Slices for extension Content/Rules for all slices
...... extension:related-artifact 0..* RelatedArtifactComponent Related Artifact for Observation component
..... code 1..1 CodeableConcept 48004-6
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48004-6
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:transcript-ref-seq 0..1 BackboneElement Reference Transcript
..... Slices for extension Content/Rules for all slices
...... extension:related-artifact 0..* RelatedArtifactComponent Related Artifact for Observation component
..... code 1..1 CodeableConcept 51958-7
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51958-7
..... value[x] 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

.... component:protein-hgvs 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... Slices for extension Content/Rules for all slices
...... extension:related-artifact 0..* RelatedArtifactComponent Related Artifact for Observation component
..... code 1..1 CodeableConcept 48005-3
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48005-3
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:protein-ref-seq 0..1 BackboneElement Protein Reference Sequence
..... Slices for extension Content/Rules for all slices
...... extension:related-artifact 0..* RelatedArtifactComponent Related Artifact for Observation component
..... code 1..1 CodeableConcept protein-ref-seq
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: protein-ref-seq
..... value[x] 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

.... component:feature-consequence 0..* BackboneElement Feature Consequence
..... Slices for extension Content/Rules for all slices
...... extension:related-artifact 0..* RelatedArtifactComponent Related Artifact for Observation component
..... code 1..1 CodeableConcept feature-consequence
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: feature-consequence
..... value[x] 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence Value Set (extensible): Concepts in sequence ontology under SO:0001537.

.... component:functional-effect 0..1 BackboneElement Functional Effect
..... Slices for extension Content/Rules for all slices
...... extension:related-artifact 0..* RelatedArtifactComponent Related Artifact for Observation component
..... code 1..1 CodeableConcept functional-effect
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: functional-effect
..... value[x] 1..1 CodeableConcept gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect Value Set (extensible): Sequence Ontology terms under SO:0001536


doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSetURI
Observation.component:coding-hgvs.value[x]requiredHGVSVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs
from this IG
Observation.component:transcript-ref-seq.value[x]example
Observation.component:protein-hgvs.value[x]requiredHGVSVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs
from this IG
Observation.component:protein-ref-seq.value[x]example
Observation.component:feature-consequence.value[x]extensibleMolecularConsequenceVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-consequence-vs
from this IG
Observation.component:functional-effect.value[x]extensibleFunctionalEffectVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/functional-effect-vs
from this IG
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C 0..* GenomicImplication Molecular Consequence
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension Content/Rules for all slices
.... 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: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.


.... body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
.... workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... 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.


.... category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
.... category:geCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: GE
... code Σ 1..1 CodeableConcept molecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: molecular-consequence
... Slices for derivedFrom Σ 1..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
.... derivedFrom:variant Σ 0..* Reference(Variant) Variant the implication is derived from
.... derivedFrom:genotype Σ 0..* Reference(Genotype) Genotype the implication is derived from
.... derivedFrom:haplotype Σ 0..* Reference(Haplotype) Haplotype the implication is derived from
.... derivedFrom:biomarker Σ 0..* Reference(Molecular Biomarker) MolecularBiomarker the implication is derived from
... Slices for component Σ 0..* BackboneElement Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... component:conclusion-string Σ 0..1 BackboneElement Clinical Conclusion
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: conclusion-string
.... component:evidence-level Σ 0..* BackboneElement Level of Evidence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 93044-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 93044-6
..... value[x] Σ 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

.... component:clinical-significance Σ 0..1 BackboneElement Clinical significance
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 53037-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 53037-8
..... value[x] Σ 1..1 CodeableConcept Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (example)
.... component:coding-hgvs Σ 0..1 BackboneElement DNA change (c.HGVS)
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48004-6
..... value[x] Σ 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:transcript-ref-seq Σ 0..1 BackboneElement Reference Transcript
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51958-7
..... value[x] Σ 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

.... component:protein-hgvs Σ 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48005-3
..... value[x] Σ 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:protein-ref-seq Σ 0..1 BackboneElement Protein Reference Sequence
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept protein-ref-seq
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: protein-ref-seq
..... value[x] Σ 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

.... component:feature-consequence Σ 0..* BackboneElement Feature Consequence
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept feature-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: feature-consequence
..... value[x] Σ 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence Value Set (extensible): Concepts in sequence ontology under SO:0001537.

.... component:functional-effect Σ 0..1 BackboneElement Functional Effect
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept functional-effect
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: functional-effect
..... value[x] Σ 1..1 CodeableConcept gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect Value Set (extensible): Sequence Ontology terms under SO:0001536


doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexamplePattern: molecular-consequence
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:evidence-level.codeexamplePattern: LOINC Code 93044-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:evidence-level.value[x]exampleEvidenceLevelExampleVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/evidence-level-example-vs
from this IG
Observation.component:clinical-significance.codeexamplePattern: LOINC Code 53037-8
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:clinical-significance.value[x]exampleLOINC LL4034-6
http://loinc.org/vs/LL4034-6
Observation.component:coding-hgvs.codeexamplePattern: LOINC Code 48004-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:coding-hgvs.value[x]requiredHGVSVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs
from this IG
Observation.component:transcript-ref-seq.codeexamplePattern: LOINC Code 51958-7
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:transcript-ref-seq.value[x]example
Observation.component:protein-hgvs.codeexamplePattern: LOINC Code 48005-3
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:protein-hgvs.value[x]requiredHGVSVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs
from this IG
Observation.component:protein-ref-seq.codeexamplePattern: protein-ref-seq
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:protein-ref-seq.value[x]example
Observation.component:feature-consequence.codeexamplePattern: feature-consequence
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:feature-consequence.value[x]extensibleMolecularConsequenceVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-consequence-vs
from this IG
Observation.component:functional-effect.codeexamplePattern: functional-effect
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:functional-effect.value[x]extensibleFunctionalEffectVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/functional-effect-vs
from this IG

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource
: contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4errorObservationIf a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
: contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
: value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C 0..* GenomicImplication Molecular Consequence
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguages Max Binding
... text 0..1 Narrative Text summary of the resource, for human interpretation
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by pattern:url
.... 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: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.


.... body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
.... workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Business Identifier for observation
... basedOn Σ 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
... partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) Part of referenced event
... status ?!Σ 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an 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.


.... category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text Σ 0..1 string Plain text representation of the concept
.... category:geCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: GE
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text Σ 0..1 string Plain text representation of the concept
... code Σ 1..1 CodeableConcept molecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
..... version 0..1 string Version of the system - if relevant
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: molecular-consequence
..... display 0..1 string Representation defined by the system
..... userSelected 0..1 boolean If this coding was chosen directly by the user
.... text 0..1 string Plain text representation of the concept
... subject Σ 0..1 Reference(Patient | Group | Device | Location) Who and/or what the observation is about
... focus Σ 0..* Reference(Resource) What the observation is about, when it is not about the subject of record
... encounter Σ 0..1 Reference(Encounter) Healthcare event during which this observation is made
... effective[x] Σ 0..1 Clinically relevant time/time-period for observation
.... effectiveDateTime dateTime
.... effectivePeriod Period
.... effectiveTiming Timing
.... effectiveInstant instant
... issued Σ 0..1 instant Date/Time this version was made available
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Who is responsible for the observation
... dataAbsentReason C 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


... note 0..* CodedAnnotation Comments about the Observation that also contain a coded type
... bodySite 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

... method 0..1 CodeableConcept How it was done
Binding: ObservationMethods (example): Methods for simple observations.

... specimen 0..1 Reference(Specimen) Specimen used for this observation
... device 0..1 Reference(Device | DeviceMetric) (Measurement) Device
... referenceRange C 0..* BackboneElement Provides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... low C 0..1 SimpleQuantity Low Range, if relevant
.... high C 0..1 SimpleQuantity High Range, if relevant
.... type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.

.... appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.


.... age 0..1 Range Applicable age range, if relevant
.... text 0..1 string Text based reference range in an observation
... hasMember Σ 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Related resource that belongs to the Observation group
... Slices for derivedFrom Σ 1..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
.... derivedFrom:variant Σ 0..* Reference(Variant) Variant the implication is derived from
.... derivedFrom:genotype Σ 0..* Reference(Genotype) Genotype the implication is derived from
.... derivedFrom:haplotype Σ 0..* Reference(Haplotype) Haplotype the implication is derived from
.... derivedFrom:biomarker Σ 0..* Reference(Molecular Biomarker) MolecularBiomarker the implication is derived from
... Slices for component Σ 0..* BackboneElement Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1 string Unique id for inter-element referencing
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

..... value[x] Σ 0..1 Actual component result
...... valueQuantity Quantity
...... valueCodeableConcept CodeableConcept
...... valueString string
...... valueBoolean boolean
...... valueInteger integer
...... valueRange Range
...... valueRatio Ratio
...... valueSampledData SampledData
...... valueTime time
...... valueDateTime dateTime
...... valuePeriod Period
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:conclusion-string Σ 0..1 BackboneElement Clinical Conclusion
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: conclusion-string
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Summary conclusion (interpretation/impression)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:evidence-level Σ 0..* BackboneElement Level of Evidence
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Extension
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 93044-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 93044-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 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

..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:clinical-significance Σ 0..1 BackboneElement Clinical significance
..... id 0..1 string Unique id for inter-element referencing
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 53037-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 53037-8
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (example)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:coding-hgvs Σ 0..1 BackboneElement DNA change (c.HGVS)
..... id 0..1 string Unique id for inter-element referencing
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48004-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:transcript-ref-seq Σ 0..1 BackboneElement Reference Transcript
..... id 0..1 string Unique id for inter-element referencing
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51958-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:protein-hgvs Σ 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... id 0..1 string Unique id for inter-element referencing
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48005-3
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:protein-ref-seq Σ 0..1 BackboneElement Protein Reference Sequence
..... id 0..1 string Unique id for inter-element referencing
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept protein-ref-seq
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: protein-ref-seq
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:feature-consequence Σ 0..* BackboneElement Feature Consequence
..... id 0..1 string Unique id for inter-element referencing
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept feature-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: feature-consequence
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence Value Set (extensible): Concepts in sequence ontology under SO:0001537.

..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:functional-effect Σ 0..1 BackboneElement Functional Effect
..... id 0..1 string Unique id for inter-element referencing
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... Slices for extension Content/Rules for all slices
...... related-artifact 0..* RelatedArtifact Related Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept functional-effect
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: functional-effect
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept gain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect Value Set (extensible): Sequence Ontology terms under SO:0001536

..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexamplePattern: molecular-consequence
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.bodySiteexampleSNOMEDCTBodyStructures
http://hl7.org/fhir/ValueSet/body-site
from the FHIR Standard
Observation.methodexampleObservationMethods
http://hl7.org/fhir/ValueSet/observation-methods
from the FHIR Standard
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
http://hl7.org/fhir/ValueSet/referencerange-meaning
from the FHIR Standard
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
http://hl7.org/fhir/ValueSet/referencerange-appliesto
from the FHIR Standard
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:conclusion-string.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:conclusion-string.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:evidence-level.codeexamplePattern: LOINC Code 93044-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:evidence-level.value[x]exampleEvidenceLevelExampleVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/evidence-level-example-vs
from this IG
Observation.component:evidence-level.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:evidence-level.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:clinical-significance.codeexamplePattern: LOINC Code 53037-8
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:clinical-significance.value[x]exampleLOINC LL4034-6
http://loinc.org/vs/LL4034-6
Observation.component:clinical-significance.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:clinical-significance.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:coding-hgvs.codeexamplePattern: LOINC Code 48004-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:coding-hgvs.value[x]requiredHGVSVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs
from this IG
Observation.component:coding-hgvs.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:coding-hgvs.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:transcript-ref-seq.codeexamplePattern: LOINC Code 51958-7
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:transcript-ref-seq.value[x]example
Observation.component:transcript-ref-seq.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:transcript-ref-seq.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:protein-hgvs.codeexamplePattern: LOINC Code 48005-3
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:protein-hgvs.value[x]requiredHGVSVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs
from this IG
Observation.component:protein-hgvs.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:protein-hgvs.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:protein-ref-seq.codeexamplePattern: protein-ref-seq
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:protein-ref-seq.value[x]example
Observation.component:protein-ref-seq.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:protein-ref-seq.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:feature-consequence.codeexamplePattern: feature-consequence
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:feature-consequence.value[x]extensibleMolecularConsequenceVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-consequence-vs
from this IG
Observation.component:feature-consequence.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:feature-consequence.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:functional-effect.codeexamplePattern: functional-effect
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:functional-effect.value[x]extensibleFunctionalEffectVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/functional-effect-vs
from this IG
Observation.component:functional-effect.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:functional-effect.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard

Constraints

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