This page is part of the Genetic Reporting Implementation Guide (v0.1.0: STU 1 Ballot 1) based on FHIR v3.3.0. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions
The official URL for this profile is:
http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-described-variant
Described Variant is a new term that HL7 has assigned to the notion of Simple, Discrete and Structural variants. We have done this because of the difficulty of drawing a clear line between these other labels for variants. The rules are often driven by the registries to which the variants are submitted and are not necessarily consistent. The difference may be driven by testing methodology rather than a difference in the underlying genetic characteristic.
This profile allows a full description of the variant found using properties from a variety of testing approaches and allowing for a variety of descriptive mechanisms. Labs are encouraged to populate what properties they know. In future versions of this implementation guide, HL7 may provide additional guidance on what properties should be sent in which situations and may subdivide Described Variant into multiple sub-profiles with more specific purpose.
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from Computable Genetic Finding
Summary
Mandatory: 2 elements (57 nested mandatory elements)
Must-Support: 84 elements
Fixed Value: 2 elements
Structures
This structure refers to these other structures:
Slices
This structure defines the following Slices:
This structure is derived from Computable Genetic Finding
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Observation | 0..* | Described Variant (Discrete or Structural) | ||
code | S | 1..1 | CodeableConcept | Genetic variant assessment Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD-Described"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required) |
method | S | 0..1 | CodeableConcept | Sequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+ Binding: LOINC Answer List LL4048-6 (required) |
component | BackboneElement | Slice: Unordered, Open by pattern:code | ||
component | S | 0..1 | BackboneElement | Transcript DNA change (cHGVS) |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48004-6"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | DNA change type |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48019-4"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Wild type | Deletion | Duplication | Insertion | Insertion/Deletion | Inversion | Substitution | Copy number gain + Binding: LOINC Answer List LL4033-8 (required) |
component | S | 0..1 | BackboneElement | Simple var ID |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81252-9"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | dbSNP ID |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81255-2"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | Genomica DNA change (gHGVS) |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81290-9"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | Genomic source class |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48002-0"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (required) |
component | S | 0..1 | BackboneElement | Amino acid change (pHGVS) |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48005-3"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | Amino acid change type |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48006-1"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation Binding: LOINC Answer List LL380-7 (required) |
component | S | 0..1 | BackboneElement | Transcript reference sequence ID |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"51958-7"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | Genomic reference sequence ID |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48013-7"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | Allelic Frequency |
code | S | 1..1 | CodeableConcept | Allelic frequency [NFr] Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81258-6"}]} |
valueQuantity | S | 1..1 | Quantity | |
value | S | 1..1 | decimal | |
system | S | 1..1 | uri | Fixed Value: http://unitsofmeasure.org |
code | S | 1..1 | code | Fixed Value: % |
component | S | 0..1 | BackboneElement | Allelic phase |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82120-7"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | 1st set of variants is cis relation to each other | 2nd set of variants is cis relation to each other | 3rd set of variants is cis relation to each other | 4th set of variants is cis relation to each other | 5th set of variants is cis relation to each other | Maternal | Paternal | Unknown | Other, please specify Binding: LOINC Answer List LL4025-4 (required) |
component | S | 0..1 | BackboneElement | Basis for allelic phase |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82309-6"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: LOINC Answer List LL4050-2 (required) |
component | S | 0..* | BackboneElement | |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82121-5"}]} |
valueQuantity | S | 1..1 | Count | |
component | S | 0..1 | BackboneElement | Allelic state |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"53034-5"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (required) |
component | S | 0..1 | BackboneElement | Genomic structural variant copy number |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82155-3"}]} |
valueQuantity | S | 1..1 | Count | |
component | S | 0..1 | BackboneElement | Structural variant reported arrCGH [Ratio] |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81299-0"}]} |
valueQuantity | S | 1..1 | SimpleQuantity | |
component | S | 0..1 | BackboneElement | Genomic ref allele |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"69547-8"}]} |
valueString | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | |
component | S | 0..1 | BackboneElement | Genomic alt allele |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"69551-0"}]} |
valueString | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | |
component | S | 0..1 | BackboneElement | Coordinate System |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: GeneticCoordinateSystem (required) |
component | S | 0..1 | BackboneElement | Genomic Allele start-end |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81254-5"}]} |
valueRange | S | 1..1 | Range | |
low | S | 1..1 | SimpleQuantity | Genomic Allele start |
high | S | 1..1 | SimpleQuantity | Genomic Allele end |
component | S | 0..1 | BackboneElement | Structural variant length |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81300-6"}]} |
valueQuantity | S | 1..1 | Count | |
component | S | 0..1 | BackboneElement | Structural variant outer start and end |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81301-4"}]} |
valueRange | S | 1..1 | Range | |
low | S | 1..1 | SimpleQuantity | |
high | S | 1..1 | SimpleQuantity | |
component | S | 0..1 | BackboneElement | Structural variant inner start and end |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81302-2"}]} |
valueRange | S | 1..1 | Range | |
low | S | 1..1 | SimpleQuantity | |
high | S | 1..1 | SimpleQuantity | |
Documentation for this format |
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Observation | I | 0..* | Described Variant (Discrete or Structural) | |
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: Common Languages (extensible) | |
text | I | 0..1 | Narrative | Text summary of the resource, for human interpretation |
contained | 0..* | Resource | Contained, inline Resources | |
body-structure | SI | 0..1 | Reference(BodyStructure) | Extension URL: http://hl7.org/fhir/StructureDefinition/body-structure |
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
identifier | Σ | 0..* | Identifier | Business Identifier for observation |
basedOn | SΣ | 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) |
category | S | 1..* | CodeableConcept | Classification of type of observation Binding: Observation Category Codes (preferred) Required Pattern: {"coding":[{"system":"http://hl7.org/fhir/observation-category","code":"laboratory"}]} |
code | SΣ | 1..1 | CodeableConcept | Genetic variant assessment Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD-Described"}]} |
subject | SΣ | 0..1 | Reference(Patient | Group | Location) | Who and/or what this is about |
focus | Σ | 0..1 | Reference(Resource) | The "focal point" of the observation |
context | 0..1 | Reference(Encounter | EpisodeOfCare) | Healthcare event during which this observation is made | |
effective[x] | SΣ | 0..1 | dateTime, Period, Timing | Assessment of overall results |
issued | SΣ | 0..1 | instant | Assessment of deletion/duplication results |
performer | SΣ | 0..1 | Reference(Practitioner | Organization | Patient | RelatedPerson) | Genes, drugs and/or conditions tested with no findings |
value[x] | SΣI | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
comment | 0..1 | string | Comments about result | |
bodySite | 0..1 | CodeableConcept | Observed body part Binding: SNOMED CT Body Structures (example) | |
method | S | 0..1 | CodeableConcept | Sequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+ Binding: LOINC Answer List LL4048-6 (required) |
specimen | S | 1..1 | Reference(Specimen) | Specimen examined |
device | 0..1 | Reference(Device | DeviceComponent | DeviceMetric) | (Measurement) Device | |
referenceRange | I | 0..* | BackboneElement | Provides guide for interpretation obs-3: Must have at least a low or a high or text |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
low | I | 0..1 | SimpleQuantity | Low Range, if relevant |
high | I | 0..1 | SimpleQuantity | High Range, if relevant |
type | 0..1 | CodeableConcept | Reference range qualifier Binding: Observation Reference Range Meaning Codes (extensible) | |
appliesTo | 0..* | CodeableConcept | Reference range population Binding: Observation Reference Range Applies To Codes (example) | |
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 | Sequence) | Related resource that belongs to the Observation group |
derivedFrom | SΣ | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | Sequence) | Related measurements the observation is made from Slice: Unordered, Open by type:$this, pattern:resolve().code | |
derivedFrom | SΣ | 0..* | Reference(Definitional Sequence) | Sequence |
component | ΣI | BackboneElement | Component results Slice: Unordered, Open by pattern:code | |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) |
value[x] | Σ | 0..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..* | BackboneElement | Gene studied ID |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48018-6"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..* | BackboneElement | Cytogenetic (chromosome) location |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48001-2"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..* | BackboneElement | Description of ranges of DNA sequences examined |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81293-3"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Transcript DNA change (cHGVS) |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48004-6"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | DNA change type |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48019-4"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Wild type | Deletion | Duplication | Insertion | Insertion/Deletion | Inversion | Substitution | Copy number gain + Binding: LOINC Answer List LL4033-8 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Simple var ID |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81252-9"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | dbSNP ID |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81255-2"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomica DNA change (gHGVS) |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81290-9"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomic source class |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48002-0"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Amino acid change (pHGVS) |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48005-3"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Amino acid change type |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48006-1"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation Binding: LOINC Answer List LL380-7 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Transcript reference sequence ID |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"51958-7"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomic reference sequence ID |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48013-7"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Allelic Frequency |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Allelic frequency [NFr] Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81258-6"}]} |
value[x] | SΣ | 1..1 | Quantity | Actual component result |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
value | SΣ | 1..1 | decimal | Numerical value (with implicit precision) |
comparator | ?!Σ | 0..1 | code | < | <= | >= | > - how to understand the value Binding: QuantityComparator (required) |
unit | Σ | 0..1 | string | Unit representation |
system | SΣI | 1..1 | uri | System that defines coded unit form Fixed Value: http://unitsofmeasure.org |
code | SΣ | 1..1 | code | Coded form of the unit Fixed Value: % |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Allelic phase |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82120-7"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | 1st set of variants is cis relation to each other | 2nd set of variants is cis relation to each other | 3rd set of variants is cis relation to each other | 4th set of variants is cis relation to each other | 5th set of variants is cis relation to each other | Maternal | Paternal | Unknown | Other, please specify Binding: LOINC Answer List LL4025-4 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Basis for allelic phase |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82309-6"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: LOINC Answer List LL4050-2 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..* | BackboneElement | Component results |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82121-5"}]} |
valueQuantity | SI | 1..1 | Count | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Allelic state |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"53034-5"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomic structural variant copy number |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82155-3"}]} |
valueQuantity | SI | 1..1 | Count | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Structural variant reported arrCGH [Ratio] |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81299-0"}]} |
valueQuantity | SI | 1..1 | SimpleQuantity | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomic ref allele |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"69547-8"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomic alt allele |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"69551-0"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Coordinate System |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: GeneticCoordinateSystem (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomic Allele start-end |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81254-5"}]} |
value[x] | SΣ | 1..1 | Range | Actual component result |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
low | SΣ | 1..1 | SimpleQuantity | Genomic Allele start |
high | SΣ | 1..1 | SimpleQuantity | Genomic Allele end |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Structural variant length |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81300-6"}]} |
valueQuantity | SI | 1..1 | Count | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Structural variant outer start and end |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81301-4"}]} |
value[x] | SΣ | 1..1 | Range | Actual component result |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
low | SΣ | 1..1 | SimpleQuantity | Low limit |
high | SΣ | 1..1 | SimpleQuantity | High limit |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Structural variant inner start and end |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81302-2"}]} |
value[x] | SΣ | 1..1 | Range | Actual component result |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
low | SΣ | 1..1 | SimpleQuantity | Low limit |
high | SΣ | 1..1 | SimpleQuantity | High limit |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
Documentation for this format |
This structure is derived from Computable Genetic Finding
Summary
Mandatory: 2 elements (57 nested mandatory elements)
Must-Support: 84 elements
Fixed Value: 2 elements
Structures
This structure refers to these other structures:
Slices
This structure defines the following Slices:
Differential View
This structure is derived from Computable Genetic Finding
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Observation | 0..* | Described Variant (Discrete or Structural) | ||
code | S | 1..1 | CodeableConcept | Genetic variant assessment Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD-Described"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required) |
method | S | 0..1 | CodeableConcept | Sequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+ Binding: LOINC Answer List LL4048-6 (required) |
component | BackboneElement | Slice: Unordered, Open by pattern:code | ||
component | S | 0..1 | BackboneElement | Transcript DNA change (cHGVS) |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48004-6"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | DNA change type |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48019-4"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Wild type | Deletion | Duplication | Insertion | Insertion/Deletion | Inversion | Substitution | Copy number gain + Binding: LOINC Answer List LL4033-8 (required) |
component | S | 0..1 | BackboneElement | Simple var ID |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81252-9"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | dbSNP ID |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81255-2"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | Genomica DNA change (gHGVS) |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81290-9"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | Genomic source class |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48002-0"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (required) |
component | S | 0..1 | BackboneElement | Amino acid change (pHGVS) |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48005-3"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | Amino acid change type |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48006-1"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation Binding: LOINC Answer List LL380-7 (required) |
component | S | 0..1 | BackboneElement | Transcript reference sequence ID |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"51958-7"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | Genomic reference sequence ID |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48013-7"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: (unbound) (example) |
component | S | 0..1 | BackboneElement | Allelic Frequency |
code | S | 1..1 | CodeableConcept | Allelic frequency [NFr] Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81258-6"}]} |
valueQuantity | S | 1..1 | Quantity | |
value | S | 1..1 | decimal | |
system | S | 1..1 | uri | Fixed Value: http://unitsofmeasure.org |
code | S | 1..1 | code | Fixed Value: % |
component | S | 0..1 | BackboneElement | Allelic phase |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82120-7"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | 1st set of variants is cis relation to each other | 2nd set of variants is cis relation to each other | 3rd set of variants is cis relation to each other | 4th set of variants is cis relation to each other | 5th set of variants is cis relation to each other | Maternal | Paternal | Unknown | Other, please specify Binding: LOINC Answer List LL4025-4 (required) |
component | S | 0..1 | BackboneElement | Basis for allelic phase |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82309-6"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: LOINC Answer List LL4050-2 (required) |
component | S | 0..* | BackboneElement | |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82121-5"}]} |
valueQuantity | S | 1..1 | Count | |
component | S | 0..1 | BackboneElement | Allelic state |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"53034-5"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (required) |
component | S | 0..1 | BackboneElement | Genomic structural variant copy number |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82155-3"}]} |
valueQuantity | S | 1..1 | Count | |
component | S | 0..1 | BackboneElement | Structural variant reported arrCGH [Ratio] |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81299-0"}]} |
valueQuantity | S | 1..1 | SimpleQuantity | |
component | S | 0..1 | BackboneElement | Genomic ref allele |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"69547-8"}]} |
valueString | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | |
component | S | 0..1 | BackboneElement | Genomic alt allele |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"69551-0"}]} |
valueString | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | |
component | S | 0..1 | BackboneElement | Coordinate System |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD"}]} |
valueCodeableConcept | S | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Binding: GeneticCoordinateSystem (required) |
component | S | 0..1 | BackboneElement | Genomic Allele start-end |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81254-5"}]} |
valueRange | S | 1..1 | Range | |
low | S | 1..1 | SimpleQuantity | Genomic Allele start |
high | S | 1..1 | SimpleQuantity | Genomic Allele end |
component | S | 0..1 | BackboneElement | Structural variant length |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81300-6"}]} |
valueQuantity | S | 1..1 | Count | |
component | S | 0..1 | BackboneElement | Structural variant outer start and end |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81301-4"}]} |
valueRange | S | 1..1 | Range | |
low | S | 1..1 | SimpleQuantity | |
high | S | 1..1 | SimpleQuantity | |
component | S | 0..1 | BackboneElement | Structural variant inner start and end |
code | S | 1..1 | CodeableConcept | Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81302-2"}]} |
valueRange | S | 1..1 | Range | |
low | S | 1..1 | SimpleQuantity | |
high | S | 1..1 | SimpleQuantity | |
Documentation for this format |
Snapshot View
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Observation | I | 0..* | Described Variant (Discrete or Structural) | |
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: Common Languages (extensible) | |
text | I | 0..1 | Narrative | Text summary of the resource, for human interpretation |
contained | 0..* | Resource | Contained, inline Resources | |
body-structure | SI | 0..1 | Reference(BodyStructure) | Extension URL: http://hl7.org/fhir/StructureDefinition/body-structure |
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
identifier | Σ | 0..* | Identifier | Business Identifier for observation |
basedOn | SΣ | 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) |
category | S | 1..* | CodeableConcept | Classification of type of observation Binding: Observation Category Codes (preferred) Required Pattern: {"coding":[{"system":"http://hl7.org/fhir/observation-category","code":"laboratory"}]} |
code | SΣ | 1..1 | CodeableConcept | Genetic variant assessment Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD-Described"}]} |
subject | SΣ | 0..1 | Reference(Patient | Group | Location) | Who and/or what this is about |
focus | Σ | 0..1 | Reference(Resource) | The "focal point" of the observation |
context | 0..1 | Reference(Encounter | EpisodeOfCare) | Healthcare event during which this observation is made | |
effective[x] | SΣ | 0..1 | dateTime, Period, Timing | Assessment of overall results |
issued | SΣ | 0..1 | instant | Assessment of deletion/duplication results |
performer | SΣ | 0..1 | Reference(Practitioner | Organization | Patient | RelatedPerson) | Genes, drugs and/or conditions tested with no findings |
value[x] | SΣI | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
comment | 0..1 | string | Comments about result | |
bodySite | 0..1 | CodeableConcept | Observed body part Binding: SNOMED CT Body Structures (example) | |
method | S | 0..1 | CodeableConcept | Sequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+ Binding: LOINC Answer List LL4048-6 (required) |
specimen | S | 1..1 | Reference(Specimen) | Specimen examined |
device | 0..1 | Reference(Device | DeviceComponent | DeviceMetric) | (Measurement) Device | |
referenceRange | I | 0..* | BackboneElement | Provides guide for interpretation obs-3: Must have at least a low or a high or text |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
low | I | 0..1 | SimpleQuantity | Low Range, if relevant |
high | I | 0..1 | SimpleQuantity | High Range, if relevant |
type | 0..1 | CodeableConcept | Reference range qualifier Binding: Observation Reference Range Meaning Codes (extensible) | |
appliesTo | 0..* | CodeableConcept | Reference range population Binding: Observation Reference Range Applies To Codes (example) | |
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 | Sequence) | Related resource that belongs to the Observation group |
derivedFrom | SΣ | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | Sequence) | Related measurements the observation is made from Slice: Unordered, Open by type:$this, pattern:resolve().code | |
derivedFrom | SΣ | 0..* | Reference(Definitional Sequence) | Sequence |
component | ΣI | BackboneElement | Component results Slice: Unordered, Open by pattern:code | |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) |
value[x] | Σ | 0..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..* | BackboneElement | Gene studied ID |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48018-6"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..* | BackboneElement | Cytogenetic (chromosome) location |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48001-2"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..* | BackboneElement | Description of ranges of DNA sequences examined |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81293-3"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Transcript DNA change (cHGVS) |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48004-6"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | DNA change type |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48019-4"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Wild type | Deletion | Duplication | Insertion | Insertion/Deletion | Inversion | Substitution | Copy number gain + Binding: LOINC Answer List LL4033-8 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Simple var ID |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81252-9"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | dbSNP ID |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81255-2"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomica DNA change (gHGVS) |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81290-9"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomic source class |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48002-0"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Amino acid change (pHGVS) |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48005-3"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Amino acid change type |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48006-1"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation Binding: LOINC Answer List LL380-7 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Transcript reference sequence ID |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"51958-7"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomic reference sequence ID |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48013-7"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: (unbound) (example) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Allelic Frequency |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Allelic frequency [NFr] Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81258-6"}]} |
value[x] | SΣ | 1..1 | Quantity | Actual component result |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
value | SΣ | 1..1 | decimal | Numerical value (with implicit precision) |
comparator | ?!Σ | 0..1 | code | < | <= | >= | > - how to understand the value Binding: QuantityComparator (required) |
unit | Σ | 0..1 | string | Unit representation |
system | SΣI | 1..1 | uri | System that defines coded unit form Fixed Value: http://unitsofmeasure.org |
code | SΣ | 1..1 | code | Coded form of the unit Fixed Value: % |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Allelic phase |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82120-7"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | 1st set of variants is cis relation to each other | 2nd set of variants is cis relation to each other | 3rd set of variants is cis relation to each other | 4th set of variants is cis relation to each other | 5th set of variants is cis relation to each other | Maternal | Paternal | Unknown | Other, please specify Binding: LOINC Answer List LL4025-4 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Basis for allelic phase |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82309-6"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: LOINC Answer List LL4050-2 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..* | BackboneElement | Component results |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82121-5"}]} |
valueQuantity | SI | 1..1 | Count | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Allelic state |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"53034-5"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomic structural variant copy number |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82155-3"}]} |
valueQuantity | SI | 1..1 | Count | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Structural variant reported arrCGH [Ratio] |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81299-0"}]} |
valueQuantity | SI | 1..1 | SimpleQuantity | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomic ref allele |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"69547-8"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomic alt allele |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"69551-0"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Coordinate System |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD"}]} |
value[x] | SΣ | 1..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual component result Binding: GeneticCoordinateSystem (required) |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Genomic Allele start-end |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81254-5"}]} |
value[x] | SΣ | 1..1 | Range | Actual component result |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
low | SΣ | 1..1 | SimpleQuantity | Genomic Allele start |
high | SΣ | 1..1 | SimpleQuantity | Genomic Allele end |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Structural variant length |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81300-6"}]} |
valueQuantity | SI | 1..1 | Count | Actual component result |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Structural variant outer start and end |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81301-4"}]} |
value[x] | SΣ | 1..1 | Range | Actual component result |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
low | SΣ | 1..1 | SimpleQuantity | Low limit |
high | SΣ | 1..1 | SimpleQuantity | High limit |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
component | SΣI | 0..1 | BackboneElement | Structural variant inner start and end |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
extension | 0..* | Extension | Additional content defined by implementations | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
code | SΣ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINC Codes (example) Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81302-2"}]} |
value[x] | SΣ | 1..1 | Range | Actual component result |
id | 0..1 | string | xml:id (or equivalent in JSON) | |
low | SΣ | 1..1 | SimpleQuantity | Low limit |
high | SΣ | 1..1 | SimpleQuantity | High limit |
dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
interpretation | 0..1 | CodeableConcept | High, low, normal, etc. Binding: Observation Interpretation Codes (extensible) | |
referenceRange | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | ||
Documentation for this format |
Other representations of profile: Schematron
Path | Name | Conformance | ValueSet |
Observation.language | Common Languages | extensible | Common Languages |
Observation.status | ObservationStatus | required | ObservationStatus |
Observation.category | Observation Category Codes | preferred | Observation Category Codes |
Observation.code | LOINC Codes | example | LOINC Codes |
Observation.value[x] | LOINC LL1971-2 | required | LOINC LL1971-2 |
Observation.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.bodySite | SNOMED CT Body Structures | example | SNOMED CT Body Structures |
Observation.method | LOINC LL4048-6 | required | LOINC LL4048-6 |
Observation.referenceRange.type | Observation Reference Range Meaning Codes | extensible | Observation Reference Range Meaning Codes |
Observation.referenceRange.appliesTo | Observation Reference Range Applies To Codes | example | Observation Reference Range Applies To Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x].comparator | QuantityComparator | required | QuantityComparator |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.value[x] | GeneticCoordinateSystem | required | GeneticCoordinateSystem |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Observation.component.code | LOINC Codes | example | LOINC Codes |
Observation.component.dataAbsentReason | DataAbsentReason | extensible | DataAbsentReason |
Observation.component.interpretation | Observation Interpretation Codes | extensible | Observation Interpretation Codes |
Id | Path | Details | Requirements |
dom-2 | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
dom-1 | Observation | If the resource is contained in another resource, it SHALL NOT contain any narrative : contained.text.empty() | |
dom-4 | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
dom-3 | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.all(('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists()) | |
obs-7 | Observation | If Observation.code is the same as a Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where( (coding.code = %resource.code.coding.code) and (coding.system = %resource.code.coding.system)).empty() | |
obs-6 | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() | |
ele-1 | Observation.extension | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ext-1 | Observation.extension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
ele-1 | Observation.extension | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ext-1 | Observation.extension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
ele-1 | Observation.referenceRange | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
obs-3 | Observation.referenceRange | Must have at least a low or a high or text : low.exists() or high.exists() or text.exists() | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
qty-3 | Observation.component.valueQuantity | If a code for the unit is present, the system SHALL also be present : code.empty() or system.exists() | |
cnt-3 | Observation.component.valueQuantity | There SHALL be a code with a value of "1" if there is a value and it SHALL be an expression of length. If system is present, it SHALL be UCUM. If present, the value SHALL a whole number. : (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
qty-3 | Observation.component.valueQuantity | If a code for the unit is present, the system SHALL also be present : code.empty() or system.exists() | |
cnt-3 | Observation.component.valueQuantity | There SHALL be a code with a value of "1" if there is a value and it SHALL be an expression of length. If system is present, it SHALL be UCUM. If present, the value SHALL a whole number. : (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
qty-3 | Observation.component.valueQuantity | If a code for the unit is present, the system SHALL also be present : code.empty() or system.exists() | |
cnt-3 | Observation.component.valueQuantity | There SHALL be a code with a value of "1" if there is a value and it SHALL be an expression of length. If system is present, it SHALL be UCUM. If present, the value SHALL a whole number. : (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
qty-3 | Observation.component.valueQuantity | If a code for the unit is present, the system SHALL also be present : code.empty() or system.exists() | |
cnt-3 | Observation.component.valueQuantity | There SHALL be a code with a value of "1" if there is a value and it SHALL be an expression of length. If system is present, it SHALL be UCUM. If present, the value SHALL a whole number. : (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
ele-1 | Observation.component | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) |
The Described Variant has a large number of properties. However these properties fall into groups, where each group of properties has a purpose (and in some cases represents information that typically appears together). The groups of properties are described below:
These are properties that help to describe where a particular variation occurs. Some are common for all computable findings (genotypes, haplotypes, described and complex variants). Some appear on the Sequence profile as they are potentially part of the 'definition' of the sequence. Some are specific to this profile as they are specific to the observation of the sequence.
TODO: gene-studied, chromosome-location, dna-region-name TODO: variant.start, variant.end TODO: inner-start-end, outer-start-end TODO other property groups