Name Flags Card. Type Description & Constraints doco
. . Observation 0 .. * Observation
. . . extension 0 .. * Extension Slice: Unordered, Open by value:url
. . . phenotypic-feature-severity S 0..1 CodeableConcept This element is an ontology class that describes the severity of the condition e.g. subclasses of Severity (HP:0012824) or SNOMED:272141005-Severities.
URL: http://ga4gh.org/fhir/phenopackets/StructureDefinition/phenotypic-feature-severity
. . . phenotypic-feature-modifier S 0..* CodeableConcept This element is a list of ontology class elements that can be empty or contain one or more ontology terms that are intended to provide more expressive or precise descriptions of a phenotypic feature, including attributes such as positionality and external factors that tend to trigger or ameliorate the feature.
URL: http://ga4gh.org/fhir/phenopackets/StructureDefinition/phenotypic-feature-modifier
. . . phenotypic-feature-onset S 0..1 dateTime, Age, Period, Range, string, CodeableConcept This element can be used to describe the age at which a phenotypic feature was first noticed or diagnosed.
URL: http://ga4gh.org/fhir/phenopackets/StructureDefinition/phenotypic-feature-onset
Binding: Onset (required)
. . . evidence S 0..* (Complex) This element is recommended and contain one or more Evidence elements that specify how the phenotype was determined.
URL: http://ga4gh.org/fhir/phenopackets/StructureDefinition/evidence
. . . code S 1 .. 1 CodeableConcept The element represents the primary ontology class which describes the phenotype. For example Craniosynostosis (HP:0001363).
Binding: Phenotypic Feature Type (required)
. . . subject S 0 .. 1 Reference(Individual)
. . . focus 0 .. 0
. . . value[x] 0 .. 0
. . . interpretation S 1..1 CodeableConcept Binding: Phenotypic Feature Interpretation (required)
. . . note S 0 .. * Annotation This element represents a free-text description of the phenotype.
. . . specimen S 0 .. 1 Reference(Specimen)
. . . referenceRange 0 .. 0
. . . hasMember 0 .. 0
. . . component 0 .. 0

doco Documentation for this format
<status value="draft" /> <date value="2019-12-20T18:15:04+00:00" /> <publisher value="Global Alliance for Genomics and Health" /> <contact> <telecom> <system value="other" /> <value value="http://ga4gh.org" /> <rank value="1" /> </telecom> </contact> <description value="This element is intended to be used to describe a phenotype that characterizes the subject of the Phenopacket. For medical use cases the subject will generally be a patient or a proband of a study, and the phenotypes will be abnormalities described by an ontology such as the Human Phenotype Ontology. The word phenotype is used with many different meanings including disease entity, but in this context we mean an individual phenotypic feature, observed as either present or absent, with possible onset, modifiers and frequency." /> <fhirVersion value="4.0.1" /> <mapping> <identity value="workflow" /> <uri value="http://hl7.org/fhir/workflow" /> <name value="Workflow Pattern" /> </mapping> <mapping> <identity value="sct-concept" /> <uri value="http://snomed.info/conceptdomain" /> <name value="SNOMED CT Concept Domain Binding" /> </mapping> <mapping> <identity value="v2" /> <uri value="http://hl7.org/v2" /> <name value="HL7 v2 Mapping" /> </mapping> <mapping> <identity value="rim" /> <uri value="http://hl7.org/v3" /> <name value="RIM Mapping" /> </mapping> <mapping> <identity value="w5" /> <uri value="http://hl7.org/fhir/fivews" /> <name value="FiveWs Pattern Mapping" /> </mapping> <mapping> <identity value="sct-attr" /> <uri value="http://snomed.org/attributebinding" /> <name value="SNOMED CT Attribute Binding" /> </mapping> <kind value="resource" /> <abstract value="false" /> <type value="Observation" /> <baseDefinition value="http://hl7.org/fhir/StructureDefinition/Observation" /> <derivation value="constraint" /> <snapshot /> <differential> <element id="Observation"> <path value="Observation" /> </element> <element id="Observation.extension"> <path value="Observation.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <ordered value="false" /> <rules value="open" /> </slicing> </element> <element id="Observation.extension:phenotypic-feature-severity"> <path value="Observation.extension" /> <sliceName value="phenotypic-feature-severity" /> <sliceIsConstraining value="false" /> <label value="severity" /> <short value="This element is an ontology class that describes the severity of the condition e.g. subclasses of Severity (HP:0012824) or SNOMED:272141005-Severities." /> <definition value="This element is an ontology class that describes the severity of the condition e.g. subclasses of Severity (HP:0012824) or SNOMED:272141005-Severities." /> <max value="1" /> <type> <code value="Extension" /> <profile value="http://ga4gh.org/fhir/phenopackets/StructureDefinition/phenotypic-feature-severity" /> </type> <mustSupport value="true" /> </element> <element id="Observation.extension:phenotypic-feature-modifier"> <path value="Observation.extension" /> <sliceName value="phenotypic-feature-modifier" /> <sliceIsConstraining value="false" /> <label value="modifiers" /> <short value="This element is a list of ontology class elements that can be empty or contain one or more ontology terms that are intended to provide more expressive or precise descriptions of a phenotypic feature, including attributes such as positionality and external factors that tend to trigger or ameliorate the feature." /> <definition value="This element is a list of ontology class elements that can be empty or contain one or more ontology terms that are intended to provide more expressive or precise descriptions of a phenotypic feature, including attributes such as positionality and external factors that tend to trigger or ameliorate the feature. Terms can be taken from the hierarchy of Clinical modifier in the HPO (noting that severity should be coded in the severity element)." /> <max value="*" /> <type> <code value="Extension" /> <profile value="http://ga4gh.org/fhir/phenopackets/StructureDefinition/phenotypic-feature-modifier" /> </type> <mustSupport value="true" /> </element> <element id="Observation.extension:phenotypic-feature-onset"> <path value="Observation.extension" /> <sliceName value="phenotypic-feature-onset" /> <sliceIsConstraining value="false" /> <label value="onset" /> <short value="This element can be used to describe the age at which a phenotypic feature was first noticed or diagnosed." /> <definition value="This element can be used to describe the age at which a phenotypic feature was first noticed or diagnosed. For many medical use cases, either the Age subelement or an ontology class (e.g., from the HPO Onset (HP:0003674) terms) will be used." /> <max value="1" /> <type> <code value="Extension" /> <profile value="http://ga4gh.org/fhir/phenopackets/StructureDefinition/phenotypic-feature-onset" /> </type> <mustSupport value="true" /> </element> <element id="Observation.extension:evidence"> <path value="Observation.extension" /> <sliceName value="evidence" /> <sliceIsConstraining value="false" /> <label value="evidence" /> <short value="This element is recommended and contain one or more Evidence elements that specify how the phenotype was determined." /> <definition value="This element is recommended and contain one or more Evidence elements that specify how the phenotype was determined." /> <max value="*" /> <type> <code value="Extension" /> <profile value="http://ga4gh.org/fhir/phenopackets/StructureDefinition/evidence" /> </type> <mustSupport value="true" /> </element> <element id="Observation.code"> <path value="Observation.code" /> <label value="type" /> <short value="The element represents the primary ontology class which describes the phenotype. For example Craniosynostosis (HP:0001363)." /> <definition value="The element represents the primary ontology class which describes the phenotype. For example Craniosynostosis (HP:0001363)." /> <requirements value="A computable phenotype needs a code from an ontology." /> <mustSupport value="true" /> <binding> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName"> <valueString value="ObservationCode" /> </extension> <strength value="required" /> <description value="The primary ontology class which describes the phenotype." /> <valueSet value="http://ga4gh.org/fhir/phenopackets/ValueSet/phenotypic-feature-type" /> </binding> </element> <element id="Observation.subject"> <path value="Observation.subject" /> <type> <code value="Reference" /> <targetProfile value="http://ga4gh.org/fhir/phenopackets/StructureDefinition/Individual" /> </type> <mustSupport value="true" /> </element> <element id="Observation.focus"> <path value="Observation.focus" /> <requirements value="Forbidden because phenotypic features are always about an individual." /> <max value="0" /> </element> <element id="Observation.value[x]"> <path value="Observation.value[x]" /> <requirements value="Forbidden because phenotypic observations are coded and have no value." /> <min value="0" /> <max value="0" /> </element> <element id="Observation.interpretation"> <path value="Observation.interpretation" /> <min value="1" /> <max value="1" /> <mustSupport value="true" /> <binding> <strength value="required" /> <valueSet value="http://ga4gh.org/fhir/phenopackets/ValueSet/phenotypic-feature-interpretation" /> </binding> </element> <element id="Observation.note"> <path value="Observation.note" /> <label value="description" /> <short value="This element represents a free-text description of the phenotype." /> <definition value="This element represents a free-text description of the phenotype." /> <comment value="It should not be used as the primary means of describing the phenotype, but can be used to supplement the record if ontology terms are not sufficiently able to capture all the nuances. In general, the type and onset etc… fields should be used for this purpose, and this field is a last resort." /> <mustSupport value="true" /> </element> <element id="Observation.specimen"> <path value="Observation.specimen" /> <mustSupport value="true" /> </element> <element id="Observation.referenceRange"> <path value="Observation.referenceRange" /> <requirements value="Forbidden because phenotypic features are not meant to have a reference range. These might be present in other observations that are used to derive the phenotypic feature, e.g., observation of __Potassium in blood__ with outcome of __high__ linked to the phenotypic feature __Hyperkalemia__." /> <max value="0" /> </element> <element id="Observation.hasMember"> <path value="Observation.hasMember" /> <requirements value="Forbidden because phenotypic features don't have member observations." /> <max value="0" /> </element> <element id="Observation.component"> <path value="Observation.component" /> <requirements value="Forbidden because phenotypic features don't have components." /> <max value="0" /> </element> </differential> </StructureDefinition>