Specimen: Specimen

This profile describes a biopsy specimen in oncology.The two relevant data points of a single biopsy specimen for the oBDS are:
  • Tumor histology date -> collection.collectedDateTime
  • Histology submission number -> accsessionIdentifier.value
As part of the core dataset of the Medical Informatics Initiative, a biopsy specimen CAN also be created in compliance with the biopsy profile from the biobank module. https://www.medizininformatik-initiative.de/Kerndatensatz/Modul_Biobank/SpecimenBioprobe.htmlIn addition to the two data points above, the following elements must also be specified:
  • status (availability of the specimen)
  • type type of specimen (SNOMED-CT coded)

NameStatusVersionCanonicalBasis
MII_PR_Onko_Specimenactive2025.1.0https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-specimenhttp://hl7.org/fhir/StructureDefinition/Specimen

Content

idΣ0..1string
id0..1string
extensionC0..*Extension
versionIdΣ0..1id
lastUpdatedΣ0..1instant
sourceΣ0..1uri
profileS Σ0..*canonical(StructureDefinition)
securityΣ0..*CodingBinding
tagΣ0..*Coding
implicitRulesΣ ?!0..1uri
language0..1codeBinding
text0..1Narrative
contained0..*Resource
extensionC0..*Extension
modifierExtension?! C0..*Extension
identifierΣ0..*Identifier
id0..1string
extensionC0..*Extension
useΣ ?!0..1codeBinding
typeΣ0..1CodeableConceptBinding
systemΣ0..1uri
valueS Σ0..1string
periodΣ0..1Period
assignerΣ0..1Reference(Organization)
statusΣ ?!0..1codeBinding
typeΣ0..1CodeableConcept
subjectS Σ1..1Reference(Patient)
receivedTimeΣ0..1dateTime
parent0..*Reference(Specimen)
request0..*Reference(ServiceRequest)
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
collectorΣ0..1Reference(Practitioner | PractitionerRole)
collectedPeriodPeriod
collectedDateTimeS Σ0..1dateTime
durationΣ0..1Duration
quantity0..1SimpleQuantity
method0..1CodeableConcept
bodySite0..1CodeableConcept
fastingStatusCodeableConceptCodeableConcept
fastingStatusDurationDuration
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
description0..1string
procedure0..1CodeableConcept
additive0..*Reference(Substance)
timeDateTimedateTime
timePeriodPeriod
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
identifierΣ0..*Identifier
description0..1string
type0..1CodeableConcept
capacity0..1SimpleQuantity
specimenQuantity0..1SimpleQuantity
additiveCodeableConceptCodeableConcept
additiveReferenceReference(Substance)
conditionΣ0..*CodeableConceptBinding
note0..*Annotation

Histologie: Dieses Profil beschreibt eine Gewebeprobe in der Onkologie.

Query syntax is not valid. Location: select Field |Name: id, Short Description: short, Notes: comment
<StructureDefinition xmlns="http://hl7.org/fhir">
<id value="mii-pr-onko-specimen" />
<url value="https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-specimen" />
<version value="2025.1.0" />
<name value="MII_PR_Onko_Specimen" />
<title value="MII PR Onkologie Specimen" />
<status value="active" />
<publisher value="Medizininformatik Initiative" />
<system value="url" />
<value value="https://www.medizininformatik-initiative.de" />
</telecom>
</contact>
<description value="Histologie: Dieses Profil beschreibt eine Gewebeprobe in der Onkologie." />
<fhirVersion value="4.0.1" />
<identity value="oBDS" />
<name value="Mapping FHIR zu oBDS" />
</mapping>
<kind value="resource" />
<abstract value="false" />
<type value="Specimen" />
<baseDefinition value="http://hl7.org/fhir/StructureDefinition/Specimen" />
<derivation value="constraint" />
<element id="Specimen">
<path value="Specimen" />
<identity value="oBDS" />
<map value="6" />
<comment value="Histologie" />
</mapping>
</element>
<element id="Specimen.meta.profile">
<path value="Specimen.meta.profile" />
<mustSupport value="true" />
</element>
<element id="Specimen.accessionIdentifier">
<path value="Specimen.accessionIdentifier" />
<mustSupport value="true" />
</element>
<element id="Specimen.accessionIdentifier.value">
<path value="Specimen.accessionIdentifier.value" />
<short value="Histologie-Einsendenummer">
<extension url="http://hl7.org/fhir/StructureDefinition/translation">
<extension url="lang">
<valueCode value="de-DE" />
</extension>
<extension url="content">
<valueString value="Histologie-Einsendenummer" />
</extension>
</extension>
</short>
<definition value="Histologie-Einsendenummer nach 6.2 oBDS 2021">
<extension url="http://hl7.org/fhir/StructureDefinition/translation">
<extension url="lang">
<valueCode value="de-DE" />
</extension>
<extension url="content">
<valueString value="Histologie-Einsendenummer nach 6.2 oBDS 2021" />
</extension>
</extension>
</definition>
<mustSupport value="true" />
<identity value="oBDS" />
<map value="6.2" />
<comment value="Histologie-Einsendenummer" />
</mapping>
</element>
<element id="Specimen.subject">
<path value="Specimen.subject" />
<min value="1" />
<code value="Reference" />
<targetProfile value="http://hl7.org/fhir/StructureDefinition/Patient" />
</type>
<mustSupport value="true" />
</element>
<element id="Specimen.collection">
<path value="Specimen.collection" />
<mustSupport value="true" />
</element>
<element id="Specimen.collection.collected[x]">
<path value="Specimen.collection.collected[x]" />
<type value="type" />
<path value="$this" />
</discriminator>
<ordered value="false" />
<rules value="open" />
</slicing>
</element>
<element id="Specimen.collection.collected[x]:collectedDateTime">
<path value="Specimen.collection.collected[x]" />
<sliceName value="collectedDateTime" />
<short value="Tumor Histologiedatum">
<extension url="http://hl7.org/fhir/StructureDefinition/translation">
<extension url="lang">
<valueCode value="de-DE" />
</extension>
<extension url="content">
<valueString value="Tumor Histologiedatum" />
</extension>
</extension>
</short>
<definition value="Histologiedatum nach 6.1 oBDS 2021">
<extension url="http://hl7.org/fhir/StructureDefinition/translation">
<extension url="lang">
<valueCode value="de-DE" />
</extension>
<extension url="content">
<valueString value="Histologiedatum nach 6.1 oBDS 2021" />
</extension>
</extension>
</definition>
<min value="0" />
<max value="1" />
<code value="dateTime" />
</type>
<mustSupport value="true" />
<identity value="oBDS" />
<map value="6.1" />
<comment value="Tumor Histologiedatum" />
</mapping>
</element>
</differential>
</StructureDefinition>
{
"resourceType": "StructureDefinition",
"id": "mii-pr-onko-specimen",
"url": "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-specimen",
"version": "2025.1.0",
"name": "MII_PR_Onko_Specimen",
"title": "MII PR Onkologie Specimen",
"status": "active",
"publisher": "Medizininformatik Initiative",
"contact": [
{
"telecom": [
{
"system": "url",
"value": "https://www.medizininformatik-initiative.de"
}
]
}
],
"description": "Histologie: Dieses Profil beschreibt eine Gewebeprobe in der Onkologie.",
"fhirVersion": "4.0.1",
"mapping": [
{
"identity": "oBDS",
"name": "Mapping FHIR zu oBDS"
}
],
"kind": "resource",
"abstract": false,
"type": "Specimen",
"baseDefinition": "http://hl7.org/fhir/StructureDefinition/Specimen",
"derivation": "constraint",
"element": [
{
"id": "Specimen",
"path": "Specimen",
"mapping": [
{
"identity": "oBDS",
"map": "6",
"comment": "Histologie"
}
]
},
{
"id": "Specimen.meta.profile",
"path": "Specimen.meta.profile",
"mustSupport": true
},
{
"id": "Specimen.accessionIdentifier",
"path": "Specimen.accessionIdentifier",
"mustSupport": true
},
{
"id": "Specimen.accessionIdentifier.value",
"path": "Specimen.accessionIdentifier.value",
"short": "Histologie-Einsendenummer",
"_short": {
{
"url": "http://hl7.org/fhir/StructureDefinition/translation",
{
"url": "lang",
"valueCode": "de-DE"
},
{
"url": "content",
"valueString": "Histologie-Einsendenummer"
}
]
}
]
},
"definition": "Histologie-Einsendenummer nach 6.2 oBDS 2021",
{
"url": "http://hl7.org/fhir/StructureDefinition/translation",
{
"url": "lang",
"valueCode": "de-DE"
},
{
"url": "content",
"valueString": "Histologie-Einsendenummer nach 6.2 oBDS 2021"
}
]
}
]
},
"mustSupport": true,
"mapping": [
{
"identity": "oBDS",
"map": "6.2",
"comment": "Histologie-Einsendenummer"
}
]
},
{
"id": "Specimen.subject",
"path": "Specimen.subject",
"min": 1,
"type": [
{
"code": "Reference",
"http://hl7.org/fhir/StructureDefinition/Patient"
]
}
],
"mustSupport": true
},
{
"id": "Specimen.collection",
"path": "Specimen.collection",
"mustSupport": true
},
{
"id": "Specimen.collection.collected[x]",
"path": "Specimen.collection.collected[x]",
"slicing": {
{
"type": "type",
"path": "$this"
}
],
"ordered": false,
"rules": "open"
}
},
{
"id": "Specimen.collection.collected[x]:collectedDateTime",
"path": "Specimen.collection.collected[x]",
"sliceName": "collectedDateTime",
"short": "Tumor Histologiedatum",
"_short": {
{
"url": "http://hl7.org/fhir/StructureDefinition/translation",
{
"url": "lang",
"valueCode": "de-DE"
},
{
"url": "content",
"valueString": "Tumor Histologiedatum"
}
]
}
]
},
"definition": "Histologiedatum nach 6.1 oBDS 2021",
{
"url": "http://hl7.org/fhir/StructureDefinition/translation",
{
"url": "lang",
"valueCode": "de-DE"
},
{
"url": "content",
"valueString": "Histologiedatum nach 6.1 oBDS 2021"
}
]
}
]
},
"min": 0,
"max": "1",
"type": [
{
"code": "dateTime"
}
],
"mustSupport": true,
"mapping": [
{
"identity": "oBDS",
"map": "6.1",
"comment": "Tumor Histologiedatum"
}
]
}
]
}
}

Mapping dataset to FHIR
DatasetExplanationFHIR
Tumor Histologiedatum

Datum, an dem die Gewebeprobe entnommen wurde.

Specimen.collection.collectedDateTime
Histologie-Einsendenummer

Die Histologie-Einsendenummer/Auftragsnummer wird vom Pathologischen Institut beim Eingang des Präparates vergeben.

Specimen.accessionIdentifier

Mapping Unified Oncological Basic Dataset (oBDS) to FHIR
oBDSDefinitionFHIR
6HistologieSpecimen
6.2Histologie-EinsendenummerSpecimen.accessionIdentifier.value
6.1Tumor HistologiedatumSpecimen.collection.collected[x]

Search ParametersThe following search parameters are relevant for the oncology module, also in combination:
  1. The search parameter _id MUST be supported:

    Examples:

    GET [base]/Condition?_id=1234

    Application notes: Further information on searching by "_id" can be found in the FHIR base specification - section "Parameters for all resources".

  2. The search parameter "_profile" MUST be supported:

    Examples:

    GET [base]/Condition?_profile=https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-diagnose

    Application notes: Further information on searching by "_profile" can be found in the FHIR base specification - section "token".

Examples
{
"resourceType": "Specimen",
"id": "mii-exa-onko-specimen-1",
"meta": {
"profile": [
"https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-specimen"
]
},
"subject": {
"reference": "Patient/example"
},
"collectedDateTime": "2021-03-14"
},
"value": "357532265"
}
}