2nd DSTU Draft For Comment

This page is part of the FHIR Specification (v0.4.0: DSTU 2 Draft). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions

Profile: Genetics

The official URL for this profile is: 

http://hl7.org/fhir/Profile/observation-genetics-cg-prf-1a-genetics

. Describes how the observation resource is used to report structured genetic test results : Standard Profile for Genetics

This profile was published on Sun, Dec 7, 2014 00:00+1100 as a draft by Mollie Ullman-Cullere.

unable to summarise extension (wrong count)

Formal Views of Profile Content

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

Differential View

This structure is derived from Observation.

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 1..1
... extension 0..1ExtensionThe Genome Build used for reference, with version number if used.
... extension 0..1ExtensionThe chromosome containing the variant.
... extension 0..1ExtensionThe genomic reference sequence identifier.
... extension 0..1ExtensionNucleotide location start
... extension 0..1ExtensionNucleotide location end
... extension 0..1ExtensionNucleotides at location on reference sequence. Use '-' for insertions.
... extension 0..1ExtensionOserved nucleotides at genomic location. Use '-' for delections.
... extension 0..1ExtensionHGNC gene symbol and identifier.
... extension 0..1ExtensionReference identifier for cDNA transcript, with version.
... extension 0..1ExtensioncDNA variant following HGVS nomenclature and identifiers.
... extension 0..1ExtensionExonic location of variant.
... extension 0..1ExtensionType of variation expressed using Sequence Ontology or LOINC codes.
... extension 0..1ExtensionReference identifier for protein transcript, with version.
... extension 0..1ExtensionProtein variant following HGVS nomenclature and identifiers.
... extension 0..1ExtensionType of protien variation expressed using Sequence Ontology or LOINC codes.
... extension 0..1ExtensionCommon name
... extension 0..1ExtensionGenomic source of the variant
... extension 0..1ExtensionVariant allelic state

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I1..1Measurements and simple assertions
obs-6: Shall only be present if Observation.value[x] is not present
... id 0..1idLogical id of this artefact
... meta 0..1MetaMetadata about the resource
... implicitRules M0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: Language (required, not extensible)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..1ExtensionThe Genome Build used for reference, with version number if used.
... extension 0..1ExtensionThe chromosome containing the variant.
... extension 0..1ExtensionThe genomic reference sequence identifier.
... extension 0..1ExtensionNucleotide location start
... extension 0..1ExtensionNucleotide location end
... extension 0..1ExtensionNucleotides at location on reference sequence. Use '-' for insertions.
... extension 0..1ExtensionOserved nucleotides at genomic location. Use '-' for delections.
... extension 0..1ExtensionHGNC gene symbol and identifier.
... extension 0..1ExtensionReference identifier for cDNA transcript, with version.
... extension 0..1ExtensioncDNA variant following HGVS nomenclature and identifiers.
... extension 0..1ExtensionExonic location of variant.
... extension 0..1ExtensionType of variation expressed using Sequence Ontology or LOINC codes.
... extension 0..1ExtensionReference identifier for protein transcript, with version.
... extension 0..1ExtensionProtein variant following HGVS nomenclature and identifiers.
... extension 0..1ExtensionType of protien variation expressed using Sequence Ontology or LOINC codes.
... extension 0..1ExtensionCommon name
... extension 0..1ExtensionGenomic source of the variant
... extension 0..1ExtensionVariant allelic state
... modifierExtension 0..*ExtensionExtensions that cannot be ignored
... code 1..1CodeableConceptType of observation (code / type)
Binding: ObservationType (example, extensible)
... value[x] 0..1Quantity, CodeableConcept, Attachment, Ratio, dateTime, Period, SampledData, string, timeActual result
... dataAbsentReason I0..1codeunknown | asked | temp | notasked +
Binding: DataAbsentReason (required, not extensible)
Example: unknown
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretation (preferred, extensible)
... comments 0..1stringComments about result
... applies[x] 0..1dateTime, PeriodPhysiologically Relevant time/time-period for observation
... issued 0..1instantDate/Time this was made available
... status M1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required, not extensible)
... reliability M0..1codeok | ongoing | early | questionable | calibrating | error +
Binding: ObservationReliability (required, not extensible)
... bodySite[x] 0..1CodeableConcept, BodySiteObserved body part
Binding: BodySite (example, extensible)
... method 0..1CodeableConceptHow it was done
Binding: ObservationMethod (example, extensible)
... identifier 0..1IdentifierUnique Id for this particular observation
... subject 0..1Patient, Group, Device, LocationWho and/or what this is about
... specimen 0..1SpecimenSpecimen used for this observation
... performer 0..*Practitioner, Organization, Patient, RelatedPersonWho did the observation
... device 0..1Device, DeviceMetric(Measurement) Device
... encounter 0..1EncounterHealthcare event during which this observation is made
... referenceRange I0..*Provides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension 0..*ExtensionExtensions that cannot be ignored
.... low I0..1QuantityLow Range, if relevant
obs-4: Low range comparators can only be '>' or '>=' or empty
.... high I0..1QuantityHigh Range, if relevant
obs-5: High range comparators can only be '<' or '<=' or empty
.... meaning 0..1CodeableConceptIndicates the meaning/use of this range of this range
Binding: ObservationRangeMeaning (example, extensible)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... related 0..*Observations related to this observation
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension 0..*ExtensionExtensions that cannot be ignored
.... type 0..1codehas-component | has-member | derived-from | sequel-to | replaces | qualified-by | interfered-by
Binding: ObservationRelationshipType (required, not extensible)
.... target 1..1ObservationObservation that is related to this one

XML Template

JSON Template

todo

Differential View

This structure is derived from Observation.

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 1..1
... extension 0..1ExtensionThe Genome Build used for reference, with version number if used.
... extension 0..1ExtensionThe chromosome containing the variant.
... extension 0..1ExtensionThe genomic reference sequence identifier.
... extension 0..1ExtensionNucleotide location start
... extension 0..1ExtensionNucleotide location end
... extension 0..1ExtensionNucleotides at location on reference sequence. Use '-' for insertions.
... extension 0..1ExtensionOserved nucleotides at genomic location. Use '-' for delections.
... extension 0..1ExtensionHGNC gene symbol and identifier.
... extension 0..1ExtensionReference identifier for cDNA transcript, with version.
... extension 0..1ExtensioncDNA variant following HGVS nomenclature and identifiers.
... extension 0..1ExtensionExonic location of variant.
... extension 0..1ExtensionType of variation expressed using Sequence Ontology or LOINC codes.
... extension 0..1ExtensionReference identifier for protein transcript, with version.
... extension 0..1ExtensionProtein variant following HGVS nomenclature and identifiers.
... extension 0..1ExtensionType of protien variation expressed using Sequence Ontology or LOINC codes.
... extension 0..1ExtensionCommon name
... extension 0..1ExtensionGenomic source of the variant
... extension 0..1ExtensionVariant allelic state

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I1..1Measurements and simple assertions
obs-6: Shall only be present if Observation.value[x] is not present
... id 0..1idLogical id of this artefact
... meta 0..1MetaMetadata about the resource
... implicitRules M0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: Language (required, not extensible)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..1ExtensionThe Genome Build used for reference, with version number if used.
... extension 0..1ExtensionThe chromosome containing the variant.
... extension 0..1ExtensionThe genomic reference sequence identifier.
... extension 0..1ExtensionNucleotide location start
... extension 0..1ExtensionNucleotide location end
... extension 0..1ExtensionNucleotides at location on reference sequence. Use '-' for insertions.
... extension 0..1ExtensionOserved nucleotides at genomic location. Use '-' for delections.
... extension 0..1ExtensionHGNC gene symbol and identifier.
... extension 0..1ExtensionReference identifier for cDNA transcript, with version.
... extension 0..1ExtensioncDNA variant following HGVS nomenclature and identifiers.
... extension 0..1ExtensionExonic location of variant.
... extension 0..1ExtensionType of variation expressed using Sequence Ontology or LOINC codes.
... extension 0..1ExtensionReference identifier for protein transcript, with version.
... extension 0..1ExtensionProtein variant following HGVS nomenclature and identifiers.
... extension 0..1ExtensionType of protien variation expressed using Sequence Ontology or LOINC codes.
... extension 0..1ExtensionCommon name
... extension 0..1ExtensionGenomic source of the variant
... extension 0..1ExtensionVariant allelic state
... modifierExtension 0..*ExtensionExtensions that cannot be ignored
... code 1..1CodeableConceptType of observation (code / type)
Binding: ObservationType (example, extensible)
... value[x] 0..1Quantity, CodeableConcept, Attachment, Ratio, dateTime, Period, SampledData, string, timeActual result
... dataAbsentReason I0..1codeunknown | asked | temp | notasked +
Binding: DataAbsentReason (required, not extensible)
Example: unknown
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretation (preferred, extensible)
... comments 0..1stringComments about result
... applies[x] 0..1dateTime, PeriodPhysiologically Relevant time/time-period for observation
... issued 0..1instantDate/Time this was made available
... status M1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required, not extensible)
... reliability M0..1codeok | ongoing | early | questionable | calibrating | error +
Binding: ObservationReliability (required, not extensible)
... bodySite[x] 0..1CodeableConcept, BodySiteObserved body part
Binding: BodySite (example, extensible)
... method 0..1CodeableConceptHow it was done
Binding: ObservationMethod (example, extensible)
... identifier 0..1IdentifierUnique Id for this particular observation
... subject 0..1Patient, Group, Device, LocationWho and/or what this is about
... specimen 0..1SpecimenSpecimen used for this observation
... performer 0..*Practitioner, Organization, Patient, RelatedPersonWho did the observation
... device 0..1Device, DeviceMetric(Measurement) Device
... encounter 0..1EncounterHealthcare event during which this observation is made
... referenceRange I0..*Provides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension 0..*ExtensionExtensions that cannot be ignored
.... low I0..1QuantityLow Range, if relevant
obs-4: Low range comparators can only be '>' or '>=' or empty
.... high I0..1QuantityHigh Range, if relevant
obs-5: High range comparators can only be '<' or '<=' or empty
.... meaning 0..1CodeableConceptIndicates the meaning/use of this range of this range
Binding: ObservationRangeMeaning (example, extensible)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... related 0..*Observations related to this observation
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension 0..*ExtensionExtensions that cannot be ignored
.... type 0..1codehas-component | has-member | derived-from | sequel-to | replaces | qualified-by | interfered-by
Binding: ObservationRelationshipType (required, not extensible)
.... target 1..1ObservationObservation that is related to this one

XML Template

JSON Template

todo

 

Other definitions: (todo)

Terminology Bindings

PathNameConformanceValueSet
Observation.languageLanguagerequiredhttp://tools.ietf.org/html/bcp47
Observation.codeObservationTypeexample (extensible)LOINC Codes
Observation.dataAbsentReasonDataAbsentReasonrequiredDataAbsentReason
Observation.interpretationObservationInterpretationpreferred (extensible)Observation Interpretation Codes
Observation.statusObservationStatusrequiredObservationStatus
Observation.reliabilityObservationReliabilityrequiredObservationReliability
Observation.bodySite[x]BodySiteexample (extensible)SNOMED CT Body Structures
Observation.methodObservationMethodexample (extensible)Observation Methods
Observation.referenceRange.meaningObservationRangeMeaningexample (extensible)Observation Reference Range Meaning Codes
Observation.related.typeObservationRelationshipTyperequiredObservationRelationshipType

Constraints

IdPathNameDetails
obs-6Observationdata absent reasonShall only be present if Observation.value[x] is not present
XPath: not(exists(f:dataAbsentReason)) or (not(exists(*[starts-with(local-name(.), 'value')])))
obs-3Observation.referenceRangereference rangeMust have at least a low or a high or text
XPath: (exists(f:low) or exists(f:high)or exists(f:text))
obs-4Observation.referenceRange.lowlow range comparatorsLow range comparators can only be '>' or '>=' or empty
XPath: not(exists(f:comparator)) or boolean(f:comparator/@value = '<') or boolean(f:comparator/@value = '<=')
obs-5Observation.referenceRange.highhigh range comparatorsHigh range comparators can only be '<' or '<=' or empty
XPath: not(exists(f:comparator)) or boolean(f:comparator/@value = '>') or boolean(f:comparator/@value = '>=')
.