Phenomics Exchange for Research and Diagnostics
0.1.0 - ci-build International flag

Phenomics Exchange for Research and Diagnostics, published by HL7 International / Clinical Interoperability Council. This guide is not an authorized publication; it is the continuous build for version 0.1.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/phenomics-exchange-ig/ and changes regularly. See the Directory of published versions

Extension: Taxonomy

Official URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Taxonomy Version: 0.1.0
Draft as of 2020-02-14 Computable Name: Taxonomy

Copyright/Legal: Global Alliance for Genomics and Health

Corresponds to taxonomy (GA4GH). For resources where there may be more than one organism being studied it is advisable to indicate the taxonomic identifier of that organism, to its most specific level.

Context of Use

This extension may be used on the following element(s):

  • Element ID Biosample

Usage info

Usage:

Formal Views of Extension Content

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

This structure is derived from Extension

Summary

Simple Extension of type base64Binary, boolean, canonical, code, date, dateTime, decimal, id, instant, integer, markdown, oid, positiveInt, string, time, unsignedInt, uri, url, uuid, Address, Age, Annotation, Attachment, CodeableConcept, Coding, ContactPoint, Count, Distance, Duration, HumanName, Identifier, Money, Period, Quantity, Range, Ratio, Reference, SampledData, Signature, Timing, ContactDetail, Contributor, DataRequirement, Expression, ParameterDefinition, RelatedArtifact, TriggerDefinition, UsageContext, Dosage, Meta: Corresponds to taxonomy (GA4GH). For resources where there may be more than one organism being studied it is advisable to indicate the taxonomic identifier of that organism, to its most specific level.

NameFlagsCard.TypeDescription & Constraintsdoco
.. Extension 0..* Extension Taxonomy
... id 0..1 string Unique id for inter-element referencing
... extension 0..0
... url 1..1 uri "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Taxonomy"
.... valueBase64Binary base64Binary
.... valueBoolean boolean
.... valueCanonical canonical(Any)
.... valueCode code
.... valueDate date
.... valueDateTime dateTime
.... valueDecimal decimal
.... valueId id
.... valueInstant instant
.... valueInteger integer
.... valueMarkdown markdown
.... valueOid oid
.... valuePositiveInt positiveInt
.... valueString string
.... valueTime time
.... valueUnsignedInt unsignedInt
.... valueUri uri
.... valueUrl url
.... valueUuid uuid
.... valueAddress Address
.... valueAge Age
.... valueAnnotation Annotation
.... valueAttachment Attachment
.... valueCodeableConcept CodeableConcept
.... valueCoding Coding
.... valueContactPoint ContactPoint
.... valueCount Count
.... valueDistance Distance
.... valueDuration Duration
.... valueHumanName HumanName
.... valueIdentifier Identifier
.... valueMoney Money
.... valuePeriod Period
.... valueQuantity Quantity
.... valueRange Range
.... valueRatio Ratio
.... valueReference Reference(Any)
.... valueSampledData SampledData
.... valueSignature Signature
.... valueTiming Timing
.... valueContactDetail ContactDetail
.... valueContributor Contributor
.... valueDataRequirement DataRequirement
.... valueExpression Expression
.... valueParameterDefinition ParameterDefinition
.... valueRelatedArtifact RelatedArtifact
.... valueTriggerDefinition TriggerDefinition
.... valueUsageContext UsageContext
.... valueDosage Dosage
.... valueMeta Meta
.... value[x]:valueCodeableConcept 0..1 CodeableConcept Value of extension
Binding: Taxonomy (required)

doco Documentation for this format

This structure is derived from Extension

Summary

Simple Extension of type base64Binary, boolean, canonical, code, date, dateTime, decimal, id, instant, integer, markdown, oid, positiveInt, string, time, unsignedInt, uri, url, uuid, Address, Age, Annotation, Attachment, CodeableConcept, Coding, ContactPoint, Count, Distance, Duration, HumanName, Identifier, Money, Period, Quantity, Range, Ratio, Reference, SampledData, Signature, Timing, ContactDetail, Contributor, DataRequirement, Expression, ParameterDefinition, RelatedArtifact, TriggerDefinition, UsageContext, Dosage, Meta: Corresponds to taxonomy (GA4GH). For resources where there may be more than one organism being studied it is advisable to indicate the taxonomic identifier of that organism, to its most specific level.

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Extension 0..* Extension Taxonomy
... id 0..1 string Unique id for inter-element referencing
... extension 0..0
... url 1..1 uri "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Taxonomy"
.... valueBase64Binary base64Binary
.... valueBoolean boolean
.... valueCanonical canonical(Any)
.... valueCode code
.... valueDate date
.... valueDateTime dateTime
.... valueDecimal decimal
.... valueId id
.... valueInstant instant
.... valueInteger integer
.... valueMarkdown markdown
.... valueOid oid
.... valuePositiveInt positiveInt
.... valueString string
.... valueTime time
.... valueUnsignedInt unsignedInt
.... valueUri uri
.... valueUrl url
.... valueUuid uuid
.... valueAddress Address
.... valueAge Age
.... valueAnnotation Annotation
.... valueAttachment Attachment
.... valueCodeableConcept CodeableConcept
.... valueCoding Coding
.... valueContactPoint ContactPoint
.... valueCount Count
.... valueDistance Distance
.... valueDuration Duration
.... valueHumanName HumanName
.... valueIdentifier Identifier
.... valueMoney Money
.... valuePeriod Period
.... valueQuantity Quantity
.... valueRange Range
.... valueRatio Ratio
.... valueReference Reference(Any)
.... valueSampledData SampledData
.... valueSignature Signature
.... valueTiming Timing
.... valueContactDetail ContactDetail
.... valueContributor Contributor
.... valueDataRequirement DataRequirement
.... valueExpression Expression
.... valueParameterDefinition ParameterDefinition
.... valueRelatedArtifact RelatedArtifact
.... valueTriggerDefinition TriggerDefinition
.... valueUsageContext UsageContext
.... valueDosage Dosage
.... valueMeta Meta
.... value[x]:valueCodeableConcept 0..1 CodeableConcept Value of extension
Binding: Taxonomy (required)

doco Documentation for this format

 

Other representations of profile: CSV, Excel, Schematron

Terminology Bindings

PathConformanceValueSetURI
Extension.value[x]:valueCodeableConceptrequiredTaxonomy (a valid code from http://purl.obolibrary.org/obo/ncbitaxon.owl)
http://hl7.org/fhir/uv/phenomics-exchange/ValueSet/Taxonomy
from this IG

Constraints

IdGradePath(s)DetailsRequirements
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()