minimal Common Oncology Data Elements (mCODE) Implementation Guide, published by HL7 International / Clinical Interoperability Council. This guide is not an authorized publication; it is the continuous build for version 4.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/fhir-mCODE-ig/ and changes regularly. See the Directory of published versions
Official URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-variant | Version: 4.0.0 | |||
Active as of 2024-12-03 | Maturity Level: 1 | Computable Name: GenomicVariant | ||
Other Identifiers: OID:2.16.840.1.113883.4.642.40.15.42.19 |
Details about a set of changes in the tested sample compared to a reference sequence. The term variant can be used to describe an alteration that may be benign, pathogenic, or of unknown significance. The term variant is increasingly being used in place of the term mutation. Variants can be computed relative to reference sequence assembly from which it was identified.
GenomicVariant SHOULD be sent as part of a GenomicsReport and MAY be sent as a standalone observation.
Observation resources associated with an in-scope patient with Observation.code
LOINC 69548-6
SHALL conform to this profile. Beyond this requirement, a producer of resources SHOULD ensure that any resource instance associated with an in-scope patient that would reasonably be expected to conform to this profile SHOULD be published in this form.
Usage:
Changes since version true:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from Variant
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Observation | 0..* | Variant | Variant | |
status | S | 1..1 | code | registered | preliminary | final | amended + |
category | S | 1..* | CodeableConcept | Classification of type of observation |
Slices for category | Content/Rules for all slices | |||
category:labCategory | 1..1 | CodeableConcept | Classification of type of observation 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://terminology.hl7.org/CodeSystem/observation-category | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
coding | 1..1 | Coding | Code defined by a terminology system | |
code | S | 1..1 | CodeableConcept | 69548-6 |
subject | S | 0..1 | Reference(Cancer Patient Profile) | Who and/or what the observation is about |
Slices for effective[x] | S | 0..1 | dateTime, Period, Timing, instant | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this |
effective[x]:effectiveDateTime | S | 0..1 | dateTime | Clinically relevant time/time-period for observation |
value[x] | S | 0..1 | CodeableConcept | Actual result |
dataAbsentReason | S | 0..1 | CodeableConcept | Why the result is missing |
method | S | 0..1 | CodeableConcept | Sequencing | SNP array | PCR | Computational analysis | ... |
specimen | S | 0..1 | Reference(Human Specimen Profile) | Specimen used for this observation |
referenceRange | 0..* | BackboneElement | Not used in this profile | |
hasMember | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Not used in this profile | |
component | S | 0..* | BackboneElement | Component results |
Slices for component | Content/Rules for all slices | |||
component:gene-studied | S | 0..* | BackboneElement | Gene Studied |
code | S | 1..1 | CodeableConcept | 48018-6 |
value[x] | S | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. |
component:cytogenetic-location | S | 0..* | BackboneElement | Cytogenetic (Chromosome) Location |
code | S | 1..1 | CodeableConcept | 48001-2 |
value[x] | S | 1..1 | CodeableConcept | Example: 1q21.1 |
component:genomic-hgvs | S | 0..1 | BackboneElement | Genomic (gDNA) Change - gHGVS |
code | S | 1..1 | CodeableConcept | 81290-9 |
value[x] | S | 1..1 | CodeableConcept | A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup |
component:cytogenomic-nomenclature | S | 0..1 | BackboneElement | Cytogenomic Nomenclature (ISCN) |
code | S | 1..1 | CodeableConcept | 81291-7 |
value[x] | S | 1..1 | CodeableConcept | Actual component result |
component:coding-change-type | S | 0..1 | BackboneElement | Coding DNA Change Type |
code | S | 1..1 | CodeableConcept | 48019-4 |
value[x] | S | 1..1 | CodeableConcept | deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) |
component:genomic-source-class | S | 0..1 | BackboneElement | Genomic Source Class |
code | S | 1..1 | CodeableConcept | 48002-0 |
value[x] | S | 1..1 | CodeableConcept | Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo |
component:sample-allelic-frequency | S | 0..1 | BackboneElement | Sample Allelic Frequency |
code | S | 1..1 | CodeableConcept | 81258-6 |
value[x] | S | 0..1 | Quantity | Relative frequency in the sample |
component:allelic-state | S | 0..1 | BackboneElement | Allelic State |
code | S | 1..1 | CodeableConcept | 53034-5 |
value[x] | S | 1..1 | CodeableConcept | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous |
component:variation-code | S | 0..* | BackboneElement | Variation Code |
code | S | 1..1 | CodeableConcept | 81252-9 |
value[x] | S | 1..1 | CodeableConcept | ClinVar ID or similar |
component:protein-hgvs | S | 0..1 | BackboneElement | Protein (Amino Acid) Change - pHGVS |
code | S | 1..1 | CodeableConcept | 48005-3 |
value[x] | S | 1..1 | CodeableConcept | A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys) |
component:amino-acid-change-type | S | 0..1 | BackboneElement | Amino Acid Change Type |
code | S | 1..1 | CodeableConcept | 48006-1 |
value[x] | S | 1..1 | CodeableConcept | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent |
component:molecular-consequence | S | 0..1 | BackboneElement | Molecular Consequence |
code | S | 1..1 | CodeableConcept | molecular-consequence |
value[x] | S | 1..1 | CodeableConcept | stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many) |
component:copy-number | S | 0..1 | BackboneElement | Genomic Structural Variant Copy Number |
code | S | 1..1 | CodeableConcept | 82155-3 |
value[x] | S | 0..1 | Quantity | Actual component result |
Documentation for this format |
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Observation | C | 0..* | Variant | Variant 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 | |
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
status | ?!SΣ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. |
Slices for category | S | 1..* | 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. 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://terminology.hl7.org/CodeSystem/observation-category | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
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 | |
code | SΣ | 1..1 | CodeableConcept | 69548-6 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: 69548-6 | |
subject | SΣ | 0..1 | Reference(Cancer Patient Profile) | Who and/or what the observation is about |
Slices for effective[x] | SΣ | 0..1 | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this | |
effectiveDateTime | dateTime | |||
effectivePeriod | Period | |||
effectiveTiming | Timing | |||
effectiveInstant | instant | |||
effective[x]:effectiveDateTime | SΣ | 0..1 | dateTime | Clinically relevant time/time-period for observation |
Slices for value[x] | SΣC | 0..1 | CodeableConcept | Actual result Slice: Unordered, Closed by type:$this |
value[x]:valueCodeableConcept | ΣC | 0..1 | CodeableConcept | Indeterminate | No call | Present | Absent. Binding: LOINC Answer List LL1971-2 (required) |
dataAbsentReason | SC | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
method | S | 0..1 | CodeableConcept | Sequencing | SNP array | PCR | Computational analysis | ... Binding: LOINC Answer List LL4048-6 (extensible) |
specimen | S | 0..1 | Reference(Human Specimen Profile) | Specimen used for this observation |
referenceRange | C | 0..* | BackboneElement | Not used in this profile obs-3: Must have at least a low or a high or text |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
hasMember | Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Not used in this profile |
Slices for component | SΣ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code |
component:All Slices | Content/Rules for all slices | |||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. |
component: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:gene-studied | SΣ | 0..* | BackboneElement | Gene Studied |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | SΣ | 1..1 | CodeableConcept | 48018-6 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: 48018-6 | |
value[x] | SΣ | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible) |
component:cytogenetic-location | SΣ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | SΣ | 1..1 | CodeableConcept | 48001-2 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: 48001-2 | |
value[x] | SΣ | 1..1 | CodeableConcept | Example: 1q21.1 |
component:reference-sequence-assembly | Σ | 0..* | BackboneElement | Human Reference Sequence Assembly |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | Σ | 1..1 | CodeableConcept | 62374-4 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: 62374-4 | |
value[x] | Σ | 1..1 | CodeableConcept | GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible) |
component:coding-hgvs | Σ | 0..1 | BackboneElement | Coding (cDNA) Change - cHGVS |
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:genomic-hgvs | SΣ | 0..1 | BackboneElement | Genomic (gDNA) Change - gHGVS |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | SΣ | 1..1 | CodeableConcept | 81290-9 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: 81290-9 | |
value[x] | SΣ | 1..1 | CodeableConcept | A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup Binding: Human Genome Variation Society (HGVS) Nomenclature (required) |
component:cytogenomic-nomenclature | SΣ | 0..1 | BackboneElement | Cytogenomic Nomenclature (ISCN) |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | SΣ | 1..1 | CodeableConcept | 81291-7 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: 81291-7 | |
value[x] | SΣ | 1..1 | CodeableConcept | Actual component result Binding Description (No ValueSet): (example): Binding not yet defined |
component:genomic-ref-seq | Σ | 0..1 | BackboneElement | Genomic Reference Sequence |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | Σ | 1..1 | CodeableConcept | 48013-7 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: 48013-7 | |
value[x] | Σ | 1..1 | CodeableConcept | Versioned genomic reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) |
component:transcript-ref-seq | Σ | 0..1 | BackboneElement | Reference Transcript |
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 Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) |
component:exact-start-end | Σ | 0..1 | BackboneElement | Exact Start-End |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | Σ | 1..1 | CodeableConcept | 81254-5 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: 81254-5 | |
component:inner-start-end | Σ | 0..1 | BackboneElement | Inner Start-End |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | Σ | 1..1 | CodeableConcept | 81302-2 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: 81302-2 | |
component:outer-start-end | Σ | 0..1 | BackboneElement | Outer Start-End |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | Σ | 1..1 | CodeableConcept | 81301-4 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: 81301-4 | |
component:coordinate-system | Σ | 0..1 | BackboneElement | Coordinate System |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | Σ | 1..1 | CodeableConcept | 92822-6 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: 92822-6 | |
value[x] | Σ | 1..1 | CodeableConcept | 0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible) |
component:ref-allele | Σ | 0..1 | BackboneElement | Genomic Ref Allele |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | Σ | 1..1 | CodeableConcept | 69547-8 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: 69547-8 | |
component:alt-allele | Σ | 0..1 | BackboneElement | Genomic Alt Allele |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | Σ | 1..1 | CodeableConcept | 69551-0 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: 69551-0 | |
component:coding-change-type | SΣ | 0..1 | BackboneElement | Coding DNA Change Type |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | SΣ | 1..1 | CodeableConcept | 48019-4 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: 48019-4 | |
value[x] | SΣ | 1..1 | CodeableConcept | deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072 |
component:genomic-source-class | SΣ | 0..1 | BackboneElement | Genomic Source Class |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | SΣ | 1..1 | CodeableConcept | 48002-0 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: 48002-0 | |
value[x] | SΣ | 1..1 | CodeableConcept | Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible) |
component:sample-allelic-frequency | SΣ | 0..1 | BackboneElement | Sample Allelic Frequency |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | SΣ | 1..1 | CodeableConcept | 81258-6 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: 81258-6 | |
value[x] | SΣ | 0..1 | Quantity | Relative frequency in the sample |
comparator | ?!Σ | 0..1 | code | < | <= | >= | > - how to understand the value Binding: QuantityComparator (required): How the Quantity should be understood and represented. |
component:allelic-read-depth | Σ | 0..1 | BackboneElement | Allelic Read Depth |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | Σ | 1..1 | CodeableConcept | 82121-5 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: 82121-5 | |
component:allelic-state | SΣ | 0..1 | BackboneElement | Allelic State |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | SΣ | 1..1 | CodeableConcept | 53034-5 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: 53034-5 | |
value[x] | SΣ | 1..1 | CodeableConcept | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible) |
component:variant-inheritance | Σ | 0..1 | BackboneElement | Variant Inheritance |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | Σ | 1..1 | CodeableConcept | variant-inheritance 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: variant-inheritance | |
value[x] | Σ | 1..1 | CodeableConcept | Maternal | Paternal | Unknown Binding: Variant Inheritances (extensible) |
component:variation-code | SΣ | 0..* | BackboneElement | Variation Code |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | SΣ | 1..1 | CodeableConcept | 81252-9 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: 81252-9 | |
value[x] | SΣ | 1..1 | CodeableConcept | ClinVar ID or similar Binding Description (No ValueSet): (example): Multiple bindings acceptable |
component:chromosome-identifier | Σ | 0..* | BackboneElement | Chromosome Identifier |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | Σ | 1..1 | CodeableConcept | 48000-4 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: 48000-4 | |
value[x] | Σ | 1..1 | CodeableConcept | Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required) |
component:protein-hgvs | SΣ | 0..1 | BackboneElement | Protein (Amino Acid) Change - pHGVS |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | SΣ | 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] | SΣ | 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:amino-acid-change-type | SΣ | 0..1 | BackboneElement | Amino Acid Change Type |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | SΣ | 1..1 | CodeableConcept | 48006-1 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: 48006-1 | |
value[x] | SΣ | 1..1 | CodeableConcept | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent Binding: LOINC Answer List LL380-7 (extensible) |
component:molecular-consequence | SΣ | 0..1 | BackboneElement | Molecular Consequence |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | SΣ | 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 | |
value[x] | SΣ | 1..1 | CodeableConcept | stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many) Binding: Molecular Consequence (extensible): Concepts in sequence ontology under SO:0001537. |
component:copy-number | SΣ | 0..1 | BackboneElement | Genomic Structural Variant Copy Number |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | SΣ | 1..1 | CodeableConcept | 82155-3 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: 82155-3 | |
value[x] | SΣC | 0..1 | Quantity | Actual component result cnt-3: There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. |
component:variant-confidence-status | Σ | 0..1 | BackboneElement | Variant Confidence Status |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
code | Σ | 1..1 | CodeableConcept | variant-confidence-status 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: variant-confidence-status | |
value[x] | Σ | 1..1 | CodeableConcept | High | Intermediate | Low Binding: Variant Confidence Status (required) |
Documentation for this format |
Path | Conformance | ValueSet / Code | URI |
Observation.status | required | ObservationStatushttp://hl7.org/fhir/ValueSet/observation-status|4.0.1 from the FHIR Standard | |
Observation.category | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | |
Observation.category:labCategory | preferred | Pattern: laboratoryhttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | |
Observation.code | example | Pattern: LOINC Code 69548-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.value[x]:valueCodeableConcept | required | LOINC LL1971-2http://loinc.org/vs/LL1971-2 | |
Observation.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | |
Observation.method | extensible | LOINC LL4048-6http://loinc.org/vs/LL4048-6 | |
Observation.component.code | example | LOINCCodes (a valid code from LOINC)http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:conclusion-string.code | example | Pattern: conclusion-stringhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:gene-studied.code | example | Pattern: LOINC Code 48018-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:gene-studied.value[x] | extensible | HGNCVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs | |
Observation.component:cytogenetic-location.code | example | Pattern: LOINC Code 48001-2http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:reference-sequence-assembly.code | example | Pattern: LOINC Code 62374-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:reference-sequence-assembly.value[x] | extensible | LOINC LL1040-6http://loinc.org/vs/LL1040-6 | |
Observation.component:coding-hgvs.code | example | Pattern: LOINC Code 48004-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:coding-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | |
Observation.component:genomic-hgvs.code | example | Pattern: LOINC Code 81290-9http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:genomic-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | |
Observation.component:cytogenomic-nomenclature.code | example | Pattern: LOINC Code 81291-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:cytogenomic-nomenclature.value[x] | example | ||
Observation.component:genomic-ref-seq.code | example | Pattern: LOINC Code 48013-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:genomic-ref-seq.value[x] | example | ||
Observation.component:transcript-ref-seq.code | example | Pattern: LOINC Code 51958-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:transcript-ref-seq.value[x] | example | ||
Observation.component:exact-start-end.code | example | Pattern: LOINC Code 81254-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:inner-start-end.code | example | Pattern: LOINC Code 81302-2http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:outer-start-end.code | example | Pattern: LOINC Code 81301-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:coordinate-system.code | example | Pattern: LOINC Code 92822-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:coordinate-system.value[x] | extensible | LOINC LL5323-2http://loinc.org/vs/LL5323-2 | |
Observation.component:ref-allele.code | example | Pattern: LOINC Code 69547-8http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:alt-allele.code | example | Pattern: LOINC Code 69551-0http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:coding-change-type.code | example | Pattern: LOINC Code 48019-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:coding-change-type.value[x] | extensible | DNAChangeTypeVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs | |
Observation.component:genomic-source-class.code | example | Pattern: LOINC Code 48002-0http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:genomic-source-class.value[x] | extensible | LOINC LL378-1http://loinc.org/vs/LL378-1 | |
Observation.component:sample-allelic-frequency.code | example | Pattern: LOINC Code 81258-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:sample-allelic-frequency.value[x].comparator | required | QuantityComparatorhttp://hl7.org/fhir/ValueSet/quantity-comparator|4.0.1 from the FHIR Standard | |
Observation.component:allelic-read-depth.code | example | Pattern: LOINC Code 82121-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:allelic-state.code | example | Pattern: LOINC Code 53034-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:allelic-state.value[x] | extensible | LOINC LL381-5http://loinc.org/vs/LL381-5 | |
Observation.component:variant-inheritance.code | example | Pattern: variant-inheritancehttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variant-inheritance.value[x] | extensible | VariantInheritanceVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-inheritance-vs | |
Observation.component:variation-code.code | example | Pattern: LOINC Code 81252-9http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variation-code.value[x] | example | ||
Observation.component:chromosome-identifier.code | example | Pattern: LOINC Code 48000-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:chromosome-identifier.value[x] | required | LOINC LL2938-0http://loinc.org/vs/LL2938-0 | |
Observation.component:protein-hgvs.code | example | Pattern: LOINC Code 48005-3http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:protein-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | |
Observation.component:amino-acid-change-type.code | example | Pattern: LOINC Code 48006-1http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:amino-acid-change-type.value[x] | extensible | LOINC LL380-7http://loinc.org/vs/LL380-7 | |
Observation.component:molecular-consequence.code | example | Pattern: molecular-consequencehttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:molecular-consequence.value[x] | extensible | MolecularConsequenceVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-consequence-vs | |
Observation.component:copy-number.code | example | Pattern: LOINC Code 82155-3http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variant-confidence-status.code | example | Pattern: variant-confidence-statushttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variant-confidence-status.value[x] | required | VariantConfidenceStatusVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-confidence-status-vs |
Name | Flags | Card. | Type | Description & Constraints | ||||
---|---|---|---|---|---|---|---|---|
Observation | C | 0..* | Variant | Variant 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.
| |||||
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 value: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 | |||||
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored | ||||
identifier | Σ | 0..* | Identifier | Business Identifier for observation | ||||
basedOn | Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order | ||||
partOf | Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) | Part of referenced event | ||||
status | ?!SΣ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
Slices for category | S | 1..* | 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. 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://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 | 0..1 | string | Plain text representation of the concept | |||||
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 | ||||
code | SΣ | 1..1 | CodeableConcept | 69548-6 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: 69548-6 | |||||
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 | |||||
subject | SΣ | 0..1 | Reference(Cancer Patient Profile) | 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 | ||||
Slices for effective[x] | SΣ | 0..1 | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this | |||||
effectiveDateTime | dateTime | |||||||
effectivePeriod | Period | |||||||
effectiveTiming | Timing | |||||||
effectiveInstant | instant | |||||||
effective[x]:effectiveDateTime | SΣ | 0..1 | dateTime | Clinically relevant time/time-period for observation | ||||
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 | ||||
Slices for value[x] | SΣC | 0..1 | CodeableConcept | Actual result Slice: Unordered, Closed by type:$this | ||||
value[x]:valueCodeableConcept | ΣC | 0..1 | CodeableConcept | Indeterminate | No call | Present | Absent. Binding: LOINC Answer List LL1971-2 (required) | ||||
dataAbsentReason | SC | 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 | S | 0..1 | CodeableConcept | Sequencing | SNP array | PCR | Computational analysis | ... Binding: LOINC Answer List LL4048-6 (extensible) | ||||
specimen | S | 0..1 | Reference(Human Specimen Profile) | Specimen used for this observation | ||||
device | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device | |||||
referenceRange | C | 0..* | BackboneElement | Not used in this profile 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) | Not used in this profile | ||||
derivedFrom | Σ | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from | ||||
Slices for component | SΣ | 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 | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
value[x] | Σ | 0..1 | Actual component result | |||||
valueQuantity | Quantity | |||||||
valueCodeableConcept | CodeableConcept | |||||||
valueString | string | |||||||
valueBoolean | boolean | |||||||
valueInteger | integer | |||||||
valueRange | Range | |||||||
valueRatio | Ratio | |||||||
valueSampledData | SampledData | |||||||
valueTime | time | |||||||
valueDateTime | dateTime | |||||||
valuePeriod | Period | |||||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component: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:gene-studied | SΣ | 0..* | BackboneElement | Gene Studied | ||||
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 | SΣ | 1..1 | CodeableConcept | 48018-6 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: 48018-6 | |||||
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] | SΣ | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible) | ||||
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:cytogenetic-location | SΣ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location | ||||
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 | SΣ | 1..1 | CodeableConcept | 48001-2 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: 48001-2 | |||||
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] | SΣ | 1..1 | CodeableConcept | Example: 1q21.1 | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:reference-sequence-assembly | Σ | 0..* | BackboneElement | Human Reference Sequence Assembly | ||||
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 | 62374-4 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: 62374-4 | |||||
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 | |||||