CodeX Implementation Guide: ICAREdata v0.1.2

CodeX Implementation Guide: ICAREdata v0.1.2 FHIR Profiles - Local Development build (v0.1.2). See the Directory of published versions

Specimen

 

The official URL for this profile is:

http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-Specimen

A specimen is a substance, physical object, or collection of objects, that the laboratory considers a single discrete, uniquely identified unit that is the subject of one or more steps in the laboratory workflow. A specimen may include multiple physical pieces as long as they are considered a single unit within the laboratory workflow. A specimen results from one to many specimen collection procedures, and may be contained in multiple specimen containers. Specimen may have one or more processing activities.

This profile builds on Specimen.

This profile was published on Wed Nov 06 00:00:00 CST 2019 as a draft by The MITRE Corporation.

Summary

Mandatory: 0 element (1 nested mandatory element)

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

Mapping Source

This structure represents the following mapping definition:

obf.Specimen maps to Specimen:
  Language maps to language
  ImplicitRules maps to implicitRules
  Metadata.VersionId maps to meta.versionId
  Metadata.SourceSystem maps to meta.extension
  Metadata.Profile maps to meta.profile
  Metadata.LastUpdated maps to meta.lastUpdated
  Metadata.SecurityLabel maps to meta.security
  Metadata.Tag maps to meta.tag
  Narrative maps to text
  Identifier maps to identifier
  Status maps to status
  SpecimenType maps to type
  AccessionIdentifier maps to accessionIdentifier
  CollectionSource maps to subject
  PartOf maps to parent
  ReceivedTime maps to receivedTime
  AmountOrSize maps to collection.quantity
  CollectionSite.BodyLocation.Code maps to collection.bodySite
  CollectionSite.BodyLocation.Laterality maps to collection.bodySite.extension
  CollectionSite.BodyLocation.AnatomicalOrientation maps to collection.bodySite.extension
  CollectionSite.BodyLocation.RelationToLandmark maps to collection.bodySite.extension
  CollectionTime maps to collection.collected[x]
  CollectionMethod maps to collection.method
  SpecimenContainer.Identifier maps to container.identifier
  SpecimenContainer.CommentOrDescription maps to container.description
  SpecimenContainer.Type maps to container.type
  SpecimenContainer.Capacity maps to container.capacity
  SpecimenContainer.SpecimenQuantity maps to container.specimenQuantity
  SpecimenContainer.Additive maps to container.additive[x]

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen obf-Specimen
... meta
.... extension Slice: Unordered, Open by value:url
.... obf-SourceSystem-extension 0..1uriSourceSystem
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-SourceSystem-extension
... extension Slice: Unordered, Open by value:url
... obf-SpecimenTreatment-extension 0..*(Complex)SpecimenTreatment
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-SpecimenTreatment-extension
... obf-HandlingRisk-extension 0..*CodeableConceptHandlingRisk
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-HandlingRisk-extension
... obf-SpecialHandling-extension 0..*CodeableConceptSpecialHandling
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-SpecialHandling-extension
... type 1..1Binding: http://terminology.hl7.org/ValueSet/v2-0487 (example)
... parent 0..1Reference(obf-Specimen)
... subject Reference(http://fhir.org/guides/argonaut/StructureDefinition/argo-patient | Group | http://fhir.org/guides/argonaut/StructureDefinition/argo-device | obf-Substance)
... collection
.... bodySite Binding: SNOMED CT Body Structures (preferred)
..... extension Slice: Unordered, Open by value:url
..... obf-datatype-Laterality-extension 0..1CodeableConceptLaterality
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-datatype-Laterality-extension
Binding: Laterality (extensible)
..... obf-datatype-AnatomicalOrientation-extension 0..1CodeableConceptAnatomicalOrientation
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-datatype-AnatomicalOrientation-extension
Binding: AnatomicalOrientationVS (extensible)
..... obf-datatype-RelationToLandmark-extension 0..*(Complex)RelationToLandmark
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-datatype-RelationToLandmark-extension
... container
.... additive[x]
..... additiveCodeableConceptCodeableConcept
..... additiveReferenceReference(obf-Substance)

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*obf-Specimen
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
.... obf-SourceSystem-extension 0..1uriSourceSystem
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-SourceSystem-extension
.... versionId Σ0..1idVersion specific identifier
.... lastUpdated Σ0..1instantWhen the resource version last changed
.... profile Σ0..*uriProfiles this resource claims to conform to
.... security Σ0..*CodingSecurity Labels applied to this resource
Binding: All Security Labels (extensible)
.... tag Σ0..*CodingTags applied to this resource
Binding: (unbound) (example)
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: http://tools.ietf.org/html/bcp47 (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
... obf-SpecimenTreatment-extension 0..*(Complex)SpecimenTreatment
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-SpecimenTreatment-extension
... obf-HandlingRisk-extension 0..*CodeableConceptHandlingRisk
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-HandlingRisk-extension
... obf-SpecialHandling-extension 0..*CodeableConceptSpecialHandling
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-SpecialHandling-extension
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierExternal Identifier
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required)
... type Σ1..1CodeableConceptKind of material that forms the specimen
Binding: http://terminology.hl7.org/ValueSet/v2-0487 (example)
... parent 0..1Reference(obf-Specimen)Specimen from which this specimen originated
... subject Σ1..1Reference(http://fhir.org/guides/argonaut/StructureDefinition/argo-patient | Group | http://fhir.org/guides/argonaut/StructureDefinition/argo-device | obf-Substance)Where the specimen came from. This may be from the patient(s) or from the environment or a device
... accessionIdentifier Σ0..1IdentifierIdentifier assigned by the lab
... receivedTime Σ0..1dateTimeThe time when specimen was received for processing
... collection 0..1BackboneElementCollection details
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... collector Σ0..1Reference(Practitioner)Who collected the specimen
.... comment 0..*stringCollector comments
.... collected[x] Σ0..1Collection time
..... collectedDateTimedateTime
..... collectedPeriodPeriod
.... quantity 0..1SimpleQuantityThe quantity of specimen collected
.... method 0..1CodeableConceptTechnique used to perform collection
Binding: SpecimenCollectionMethod (example)
.... bodySite 0..1CodeableConceptAnatomical collection site
Binding: SNOMED CT Body Structures (preferred)
..... id 0..1idxml:id (or equivalent in JSON)
..... extension 0..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
..... obf-datatype-Laterality-extension 0..1CodeableConceptLaterality
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-datatype-Laterality-extension
Binding: Laterality (extensible)
..... obf-datatype-AnatomicalOrientation-extension 0..1CodeableConceptAnatomicalOrientation
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-datatype-AnatomicalOrientation-extension
Binding: AnatomicalOrientationVS (extensible)
..... obf-datatype-RelationToLandmark-extension 0..*(Complex)RelationToLandmark
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-datatype-RelationToLandmark-extension
..... coding Σ0..*CodingCode defined by a terminology system
..... text Σ0..1stringPlain text representation of the concept
... treatment 0..*BackboneElementTreatment and processing step details
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... description 0..1stringTextual description of procedure
.... procedure 0..1CodeableConceptIndicates the treatment or processing step applied to the specimen
Binding: SpecimenTreatmentProcedure (example)
.... additive 0..*Reference(Substance)Material used in the processing step
... container 0..*BackboneElementDirect container of specimen (tube/slide, etc.)
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... identifier Σ0..*IdentifierId for the container
.... description 0..1stringTextual description of the container
.... type 0..1CodeableConceptKind of container directly associated with specimen
Binding: SpecimenContainer (example)
.... capacity 0..1SimpleQuantityContainer volume or size
.... specimenQuantity 0..1SimpleQuantityQuantity of specimen within container
.... additive[x] 0..1Additive associated with container
Binding: v2 Additive/Preservative (example)
..... additiveCodeableConceptCodeableConcept
..... additiveReferenceReference(obf-Substance)

doco Documentation for this format

Summary

Mandatory: 0 element (1 nested mandatory element)

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

Mapping Source

This structure represents the following mapping definition:

obf.Specimen maps to Specimen:
  Language maps to language
  ImplicitRules maps to implicitRules
  Metadata.VersionId maps to meta.versionId
  Metadata.SourceSystem maps to meta.extension
  Metadata.Profile maps to meta.profile
  Metadata.LastUpdated maps to meta.lastUpdated
  Metadata.SecurityLabel maps to meta.security
  Metadata.Tag maps to meta.tag
  Narrative maps to text
  Identifier maps to identifier
  Status maps to status
  SpecimenType maps to type
  AccessionIdentifier maps to accessionIdentifier
  CollectionSource maps to subject
  PartOf maps to parent
  ReceivedTime maps to receivedTime
  AmountOrSize maps to collection.quantity
  CollectionSite.BodyLocation.Code maps to collection.bodySite
  CollectionSite.BodyLocation.Laterality maps to collection.bodySite.extension
  CollectionSite.BodyLocation.AnatomicalOrientation maps to collection.bodySite.extension
  CollectionSite.BodyLocation.RelationToLandmark maps to collection.bodySite.extension
  CollectionTime maps to collection.collected[x]
  CollectionMethod maps to collection.method
  SpecimenContainer.Identifier maps to container.identifier
  SpecimenContainer.CommentOrDescription maps to container.description
  SpecimenContainer.Type maps to container.type
  SpecimenContainer.Capacity maps to container.capacity
  SpecimenContainer.SpecimenQuantity maps to container.specimenQuantity
  SpecimenContainer.Additive maps to container.additive[x]

Differential View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen obf-Specimen
... meta
.... extension Slice: Unordered, Open by value:url
.... obf-SourceSystem-extension 0..1uriSourceSystem
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-SourceSystem-extension
... extension Slice: Unordered, Open by value:url
... obf-SpecimenTreatment-extension 0..*(Complex)SpecimenTreatment
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-SpecimenTreatment-extension
... obf-HandlingRisk-extension 0..*CodeableConceptHandlingRisk
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-HandlingRisk-extension
... obf-SpecialHandling-extension 0..*CodeableConceptSpecialHandling
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-SpecialHandling-extension
... type 1..1Binding: http://terminology.hl7.org/ValueSet/v2-0487 (example)
... parent 0..1Reference(obf-Specimen)
... subject Reference(http://fhir.org/guides/argonaut/StructureDefinition/argo-patient | Group | http://fhir.org/guides/argonaut/StructureDefinition/argo-device | obf-Substance)
... collection
.... bodySite Binding: SNOMED CT Body Structures (preferred)
..... extension Slice: Unordered, Open by value:url
..... obf-datatype-Laterality-extension 0..1CodeableConceptLaterality
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-datatype-Laterality-extension
Binding: Laterality (extensible)
..... obf-datatype-AnatomicalOrientation-extension 0..1CodeableConceptAnatomicalOrientation
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-datatype-AnatomicalOrientation-extension
Binding: AnatomicalOrientationVS (extensible)
..... obf-datatype-RelationToLandmark-extension 0..*(Complex)RelationToLandmark
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-datatype-RelationToLandmark-extension
... container
.... additive[x]
..... additiveCodeableConceptCodeableConcept
..... additiveReferenceReference(obf-Substance)

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*obf-Specimen
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
.... obf-SourceSystem-extension 0..1uriSourceSystem
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-SourceSystem-extension
.... versionId Σ0..1idVersion specific identifier
.... lastUpdated Σ0..1instantWhen the resource version last changed
.... profile Σ0..*uriProfiles this resource claims to conform to
.... security Σ0..*CodingSecurity Labels applied to this resource
Binding: All Security Labels (extensible)
.... tag Σ0..*CodingTags applied to this resource
Binding: (unbound) (example)
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: http://tools.ietf.org/html/bcp47 (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
... obf-SpecimenTreatment-extension 0..*(Complex)SpecimenTreatment
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-SpecimenTreatment-extension
... obf-HandlingRisk-extension 0..*CodeableConceptHandlingRisk
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-HandlingRisk-extension
... obf-SpecialHandling-extension 0..*CodeableConceptSpecialHandling
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-SpecialHandling-extension
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierExternal Identifier
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required)
... type Σ1..1CodeableConceptKind of material that forms the specimen
Binding: http://terminology.hl7.org/ValueSet/v2-0487 (example)
... parent 0..1Reference(obf-Specimen)Specimen from which this specimen originated
... subject Σ1..1Reference(http://fhir.org/guides/argonaut/StructureDefinition/argo-patient | Group | http://fhir.org/guides/argonaut/StructureDefinition/argo-device | obf-Substance)Where the specimen came from. This may be from the patient(s) or from the environment or a device
... accessionIdentifier Σ0..1IdentifierIdentifier assigned by the lab
... receivedTime Σ0..1dateTimeThe time when specimen was received for processing
... collection 0..1BackboneElementCollection details
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... collector Σ0..1Reference(Practitioner)Who collected the specimen
.... comment 0..*stringCollector comments
.... collected[x] Σ0..1Collection time
..... collectedDateTimedateTime
..... collectedPeriodPeriod
.... quantity 0..1SimpleQuantityThe quantity of specimen collected
.... method 0..1CodeableConceptTechnique used to perform collection
Binding: SpecimenCollectionMethod (example)
.... bodySite 0..1CodeableConceptAnatomical collection site
Binding: SNOMED CT Body Structures (preferred)
..... id 0..1idxml:id (or equivalent in JSON)
..... extension 0..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
..... obf-datatype-Laterality-extension 0..1CodeableConceptLaterality
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-datatype-Laterality-extension
Binding: Laterality (extensible)
..... obf-datatype-AnatomicalOrientation-extension 0..1CodeableConceptAnatomicalOrientation
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-datatype-AnatomicalOrientation-extension
Binding: AnatomicalOrientationVS (extensible)
..... obf-datatype-RelationToLandmark-extension 0..*(Complex)RelationToLandmark
URL: http://mcodeinitiative.org/codex/us/icare/StructureDefinition/obf-datatype-RelationToLandmark-extension
..... coding Σ0..*CodingCode defined by a terminology system
..... text Σ0..1stringPlain text representation of the concept
... treatment 0..*BackboneElementTreatment and processing step details
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... description 0..1stringTextual description of procedure
.... procedure 0..1CodeableConceptIndicates the treatment or processing step applied to the specimen
Binding: SpecimenTreatmentProcedure (example)
.... additive 0..*Reference(Substance)Material used in the processing step
... container 0..*BackboneElementDirect container of specimen (tube/slide, etc.)
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... identifier Σ0..*IdentifierId for the container
.... description 0..1stringTextual description of the container
.... type 0..1CodeableConceptKind of container directly associated with specimen
Binding: SpecimenContainer (example)
.... capacity 0..1SimpleQuantityContainer volume or size
.... specimenQuantity 0..1SimpleQuantityQuantity of specimen within container
.... additive[x] 0..1Additive associated with container
Binding: v2 Additive/Preservative (example)
..... additiveCodeableConceptCodeableConcept
..... additiveReferenceReference(obf-Substance)

doco Documentation for this format

Downloads: StructureDefinition: (XML, JSON, TTL), Schema: XML Schematron

 

Terminology Bindings

PathConformanceValueSet
Specimen.meta.securityextensibleAll Security Labels
Specimen.meta.tagexample
Specimen.languagerequiredhttp://tools.ietf.org/html/bcp47
Specimen.statusrequiredSpecimenStatus
Specimen.typeexamplehttp://terminology.hl7.org/ValueSet/v2-0487
Specimen.collection.methodexampleSpecimenCollectionMethod
Specimen.collection.bodySitepreferredSNOMED CT Body Structures
Specimen.treatment.procedureexampleSpecimenTreatmentProcedure
Specimen.container.typeexampleSpecimenContainer
Specimen.container.additivexexamplev2 Additive/Preservative

 

Constraints

IdPathDetailsRequirements