Molekularer Biomarker: Observation


Inhalt

Dieses abstrakte Profil beschreibt einen Molekularen Biomarker im NGS-Bericht. Es basiert inhaltlich auf der Molekularen Biomarker-Definition des Clinical Genomic Reporting Implementation Guides STU3, ohne in der Kommentierungsversion davon direkt zu erben. Er ist Grundlage sowohl für die gen-übergreifenden Biomarker wie HRD, MSI, TMB und BRCAness, als auch für Immunhistochemie und In-Situ-Hybridisierung.


Verknüpfungen zu anderen Ressourcen


Zeitliche Zuordnung im Verlauf

NameStatusVersionCanonicalBasis
MII_PR_MTB_Molekularer_Biomarkerdraft2024.0.0-ballothttps://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureDefinition/mii-pr-mtb-molekularer-biomarkerhttp://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker

Inhalt

idΣ0..1id
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
basedOnΣ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)
partOfΣ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)
statusΣ ?!1..1codeBinding
id0..1string
extensionC0..*Extension
codingΣ1..1CodingPattern
textΣ0..1string
id0..1string
extensionC0..*Extension
codingΣ1..1CodingPattern
textΣ0..1string
id0..1string
extensionC0..*Extension
codingΣ1..1CodingPattern
textΣ0..1string
codeS Σ1..1CodeableConceptBinding
subjectΣ0..1Reference(Patient | Group | Device | Location)
focusS Σ0..*Reference(MII_PR_Onko_Diagnose_Primaertumor | MII_PR_MTB_Diagnose_Primaertumor)
encounterΣ0..1Reference(Encounter)
effectiveDateTimedateTime
effectivePeriodPeriod
effectiveTimingTiming
effectiveInstantinstant
issuedΣ0..1instant
performerΣ0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)
valueQuantityQuantity
valueCodeableConceptCodeableConcept
valueStringstring
valueBooleanboolean
valueIntegerinteger
valueRangeRange
valueRatioRatio
valueSampledDataSampledData
valueTimetime
valueDateTimedateTime
valuePeriodPeriod
dataAbsentReasonC0..1CodeableConceptBinding
interpretation0..*CodeableConceptBinding
note0..*Annotation
bodySite0..1CodeableConcept
method0..1CodeableConcept
specimen0..1Reference(Specimen)
device0..1Reference(Device | DeviceMetric)
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
lowC0..1SimpleQuantity
highC0..1SimpleQuantity
type0..1CodeableConceptBinding
appliesTo0..*CodeableConcept
age0..1Range
text0..1string
hasMemberΣ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)
variantΣ0..*Reference(Variant)
genotypeΣ0..*Reference(Genotype)
haplotypeΣ0..*Reference(Haplotype)
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
codeΣ1..1CodeableConcept
valueQuantityQuantity
valueCodeableConceptCodeableConcept
valueStringstring
valueBooleanboolean
valueIntegerinteger
valueRangeRange
valueRatioRatio
valueSampledDataSampledData
valueTimetime
valueDateTimedateTime
valuePeriodPeriod
dataAbsentReasonC0..1CodeableConceptBinding
interpretation0..*CodeableConceptBinding
referenceRange0..*see (referenceRange)
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
codeΣ1..1CodeableConceptPattern
valueCodeableConceptCodeableConcept
dataAbsentReasonC0..1CodeableConceptBinding
interpretation0..*CodeableConceptBinding
referenceRange0..*see (referenceRange)
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
codeΣ1..1CodeableConceptPattern
valueCodeableConceptCodeableConcept
dataAbsentReasonC0..1CodeableConceptBinding
interpretation0..*CodeableConceptBinding
referenceRange0..*see (referenceRange)

Stellt einen gefundenden Biomarker dar. Das Profil ist auf Basis von https://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-molecular-biomarker.html nachgebaut.

Feldname
Observation.meta
Observation.meta.profile
Observation.code
Observation.focus
<StructureDefinition xmlns="http://hl7.org/fhir">
<id value="mii-pr-mtb-molekularer-biomarker" />
<url value="https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureDefinition/mii-pr-mtb-molekularer-biomarker" />
<version value="2024.0.0-ballot" />
<name value="MII_PR_MTB_Molekularer_Biomarker" />
<title value="MII PR MTB Molekularer Biomarker" />
<status value="draft" />
<publisher value="Medizininformatik Initiative" />
<system value="url" />
<value value="https://www.medizininformatik-initiative.de" />
</telecom>
</contact>
<description value="Stellt einen gefundenden Biomarker dar. Das Profil ist auf Basis von https://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-molecular-biomarker.html nachgebaut." />
<fhirVersion value="4.0.1" />
<kind value="resource" />
<abstract value="false" />
<type value="Observation" />
<baseDefinition value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker" />
<derivation value="constraint" />
<element id="Observation.meta">
<path value="Observation.meta" />
<mustSupport value="true" />
</element>
<element id="Observation.meta.profile">
<path value="Observation.meta.profile" />
<mustSupport value="true" />
</element>
<element id="Observation.code">
<path value="Observation.code" />
<mustSupport value="true" />
<strength value="extensible" />
<valueSet value="https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/ValueSet/mii-vs-mtb-molekulare-biomarker" />
</binding>
</element>
<element id="Observation.focus">
<path value="Observation.focus" />
<code value="Reference" />
<targetProfile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-diagnose-primaertumor" />
<targetProfile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureDefinition/mii-pr-mtb-diagnose-primaertumor" />
</type>
<mustSupport value="true" />
</element>
</differential>
</StructureDefinition>
{
"resourceType": "StructureDefinition",
"id": "mii-pr-mtb-molekularer-biomarker",
"url": "https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureDefinition/mii-pr-mtb-molekularer-biomarker",
"version": "2024.0.0-ballot",
"name": "MII_PR_MTB_Molekularer_Biomarker",
"title": "MII PR MTB Molekularer Biomarker",
"status": "draft",
"publisher": "Medizininformatik Initiative",
"contact": [
{
"telecom": [
{
"system": "url",
"value": "https://www.medizininformatik-initiative.de"
}
]
}
],
"description": "Stellt einen gefundenden Biomarker dar. Das Profil ist auf Basis von https://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-molecular-biomarker.html nachgebaut.",
"fhirVersion": "4.0.1",
"kind": "resource",
"abstract": false,
"type": "Observation",
"baseDefinition": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker",
"derivation": "constraint",
"element": [
{
"id": "Observation.meta",
"path": "Observation.meta",
"mustSupport": true
},
{
"id": "Observation.meta.profile",
"path": "Observation.meta.profile",
"mustSupport": true
},
{
"id": "Observation.code",
"path": "Observation.code",
"mustSupport": true,
"binding": {
"strength": "extensible",
"valueSet": "https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/ValueSet/mii-vs-mtb-molekulare-biomarker"
}
},
{
"id": "Observation.focus",
"path": "Observation.focus",
"type": [
{
"code": "Reference",
"https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-diagnose-primaertumor",
"https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureDefinition/mii-pr-mtb-diagnose-primaertumor"
]
}
],
"mustSupport": true
}
]
}
}

Mapping Datensatz zu FHIR

DatensatzErklaerungFHIR
RNA Fusion

RNA Fusion

MII_PR_MTB_RNA_Seq
Varianten ID

Varianten ID

MII_PR_MTB_RNA_Seq.component[variation-code]
Entrez ID

Entrez ID

MII_PR_MTB_RNA_Seq.component[variation-code]
Ensemble ID

Ensemble ID

MII_PR_MTB_RNA_Seq.component[variation-code]
Gen

Gen

MII_PR_MTB_RNA_Seq.component[gene-studied]
Transcript ID

Transcript ID

MII_PR_MTB_RNA_Seq.component[transcript-id]
Transcripts Per Million

Transcripts Per Million

MII_PR_MTB_RNA_Seq.component[transcripts-per-million]
Tissue Corrected Expression

Tissue Corrected Expression

MII_PR_MTB_RNA_Seq.component[tissue-corrected-expression]
Raw counts

Raw counts

MII_PR_MTB_RNA_Seq.component[raw-counts]
Library size

Library size

MII_PR_MTB_RNA_Seq.component[library-size]
Cohort ranking

Cohort ranking

MII_PR_MTB_RNA_Seq.component[cohort-ranking]

Suchparameter

Folgende Suchparameter sind für das Modul Onkologie relevant, auch in Kombination:

  1. Der Suchparameter "_id" MUSS unterstützt werden:

    Beispiele:

    GET [base]/Observation?_id=12345

    Anwendungshinweise: Weitere Informationen zur Suche nach "_id" finden sich in der FHIR-Basisspezifikation - Abschnitt "Parameters for all resources".

  2. Der Suchparameter "_profile" MUSS unterstützt werden:

    Beispiele:

    GET [base]/Observation?_profile=https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureDefinition/mii-pr-mtb-molekularer-biomarker

    Anwendungshinweise: Weitere Informationen zur Suche nach "_profile" finden sich in der FHIR-Basisspezifikation - Abschnitt "Parameters for all resources".

  3. Der Suchparameter "focus" MUSS unterstützt werden:

    Beispiele:

    GET [base]/Observation?focus=Condition/example-mii-mtb-diagnose

    Anwendungshinweise: Weitere Informationen zur Suche nach "focus" finden sich in der FHIR-Basisspezifikation - Abschnitt "reference".


Beispiele