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.
Name | Status | Version | Canonical | Basis |
---|---|---|---|---|
MII_PR_MTB_Molekularer_Biomarker | draft | 2024.0.0-ballot | https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureDefinition/mii-pr-mtb-molekularer-biomarker | http://hl7.org/fhir/StructureDefinition/Observation |
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.category:labCategory |
Observation.focus |
Observation.component:biomarker-category |
<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" /> <contact> <telecom> <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/StructureDefinition/Observation" /> <derivation value="constraint" /> <differential> <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.category"> <path value="Observation.category" /> <slicing> <discriminator> <type value="value" /> <path value="coding" /> </discriminator> <description value="Slices for category" /> <ordered value="false" /> <rules value="open" /> </slicing> <min value="3" /> </element> <element id="Observation.category:labCategory"> <path value="Observation.category" /> <sliceName value="labCategory" /> <min value="1" /> <max value="1" /> <mustSupport value="true" /> </element> <element id="Observation.category:labCategory.coding"> <path value="Observation.category.coding" /> <min value="1" /> <max value="1" /> <patternCoding> <system value="http://terminology.hl7.org/CodeSystem/observation-category" /> <code value="laboratory" /> </patternCoding> </element> <element id="Observation.category:geCategory"> <path value="Observation.category" /> <sliceName value="geCategory" /> <min value="1" /> <max value="1" /> </element> <element id="Observation.category:geCategory.coding"> <path value="Observation.category.coding" /> <min value="1" /> <max value="1" /> <patternCoding> <system value="http://terminology.hl7.org/CodeSystem/v2-0074" /> <code value="GE" /> </patternCoding> </element> <element id="Observation.category:mbCategory"> <path value="Observation.category" /> <sliceName value="mbCategory" /> <min value="1" /> <max value="1" /> </element> <element id="Observation.category:mbCategory.coding"> <path value="Observation.category.coding" /> <min value="1" /> <max value="1" /> <patternCoding> <system value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" /> <code value="biomarker-category" /> </patternCoding> </element> <element id="Observation.code"> <path value="Observation.code" /> <binding> <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" /> <type> <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> <element id="Observation.derivedFrom"> <path value="Observation.derivedFrom" /> <slicing> <discriminator> <type value="profile" /> <path value="resolve()" /> </discriminator> <description value="Slices for derivedFrom" /> <ordered value="false" /> <rules value="open" /> </slicing> </element> <element id="Observation.derivedFrom:variant"> <path value="Observation.derivedFrom" /> <sliceName value="variant" /> <min value="0" /> <max value="*" /> <type> <code value="Reference" /> <targetProfile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" /> </type> </element> <element id="Observation.derivedFrom:genotype"> <path value="Observation.derivedFrom" /> <sliceName value="genotype" /> <min value="0" /> <max value="*" /> <type> <code value="Reference" /> <targetProfile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" /> </type> </element> <element id="Observation.derivedFrom:haplotype"> <path value="Observation.derivedFrom" /> <sliceName value="haplotype" /> <min value="0" /> <max value="*" /> <type> <code value="Reference" /> <targetProfile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype" /> </type> </element> <element id="Observation.component"> <path value="Observation.component" /> <slicing> <discriminator> <type value="value" /> <path value="code" /> </discriminator> <description value="Slices for component" /> <ordered value="false" /> <rules value="open" /> </slicing> </element> <element id="Observation.component:gene-studied"> <path value="Observation.component" /> <sliceName value="gene-studied" /> <min value="0" /> <max value="*" /> </element> <element id="Observation.component:gene-studied.code.coding"> <path value="Observation.component.code.coding" /> <patternCoding> <system value="http://loinc.org" /> <code value="48018-6" /> </patternCoding> </element> <element id="Observation.component:gene-studied.value[x]"> <path value="Observation.component.value[x]" /> <slicing> <discriminator> <type value="type" /> <path value="$this" /> </discriminator> <ordered value="false" /> <rules value="open" /> </slicing> </element> <element id="Observation.component:gene-studied.value[x]:valueCodeableConcept"> <path value="Observation.component.value[x]" /> <sliceName value="valueCodeableConcept" /> <short value="The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used." /> <min value="0" /> <max value="1" /> <type> <code value="CodeableConcept" /> </type> <binding> <strength value="extensible" /> <valueSet value="http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs" /> </binding> </element> <element id="Observation.component:biomarker-category"> <path value="Observation.component" /> <sliceName value="biomarker-category" /> <min value="0" /> <max value="*" /> <mustSupport value="true" /> </element> <element id="Observation.component:biomarker-category.code"> <path value="Observation.component.code" /> <patternCodeableConcept> <coding> <system value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" /> <code value="biomarker-category" /> </coding> </patternCodeableConcept> </element> <element id="Observation.component:biomarker-category.value[x]"> <path value="Observation.component.value[x]" /> <type> <code value="CodeableConcept" /> </type> <binding> <strength value="preferred" /> <valueSet value="http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-category-vs" /> </binding> </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/StructureDefinition/Observation", "derivation": "constraint", "differential": { "element": [ { "id": "Observation.meta", "path": "Observation.meta", "mustSupport": true }, { "id": "Observation.meta.profile", "path": "Observation.meta.profile", "mustSupport": true }, { "id": "Observation.category", "path": "Observation.category", "slicing": { "discriminator": [ { "type": "value", "path": "coding" } ], "rules": "open", "description": "Slices for category", "ordered": false }, "min": 3 }, { "id": "Observation.category:labCategory", "path": "Observation.category", "sliceName": "labCategory", "min": 1, "max": "1", "mustSupport": true }, { "id": "Observation.category:labCategory.coding", "path": "Observation.category.coding", "min": 1, "max": "1", "patternCoding": { "code": "laboratory", "system": "http://terminology.hl7.org/CodeSystem/observation-category" } }, { "id": "Observation.category:geCategory", "path": "Observation.category", "sliceName": "geCategory", "min": 1, "max": "1" }, { "id": "Observation.category:geCategory.coding", "path": "Observation.category.coding", "min": 1, "max": "1", "patternCoding": { "code": "GE", "system": "http://terminology.hl7.org/CodeSystem/v2-0074" } }, { "id": "Observation.category:mbCategory", "path": "Observation.category", "sliceName": "mbCategory", "min": 1, "max": "1" }, { "id": "Observation.category:mbCategory.coding", "path": "Observation.category.coding", "min": 1, "max": "1", "patternCoding": { "code": "biomarker-category", "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } }, { "id": "Observation.code", "path": "Observation.code", "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", "targetProfile": [ "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 }, { "id": "Observation.derivedFrom", "path": "Observation.derivedFrom", "slicing": { "discriminator": [ { "type": "profile", "path": "resolve()" } ], "rules": "open", "description": "Slices for derivedFrom", "ordered": false } }, { "id": "Observation.derivedFrom:variant", "path": "Observation.derivedFrom", "sliceName": "variant", "min": 0, "max": "*", "type": [ { "code": "Reference", "targetProfile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] } ] }, { "id": "Observation.derivedFrom:genotype", "path": "Observation.derivedFrom", "sliceName": "genotype", "min": 0, "max": "*", "type": [ { "code": "Reference", "targetProfile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" ] } ] }, { "id": "Observation.derivedFrom:haplotype", "path": "Observation.derivedFrom", "sliceName": "haplotype", "min": 0, "max": "*", "type": [ { "code": "Reference", "targetProfile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype" ] } ] }, { "id": "Observation.component", "path": "Observation.component", "slicing": { "discriminator": [ { "type": "value", "path": "code" } ], "rules": "open", "description": "Slices for component", "ordered": false } }, { "id": "Observation.component:gene-studied", "path": "Observation.component", "sliceName": "gene-studied", "min": 0, "max": "*" }, { "id": "Observation.component:gene-studied.code.coding", "path": "Observation.component.code.coding", "patternCoding": { "code": "48018-6", "system": "http://loinc.org" } }, { "id": "Observation.component:gene-studied.value[x]", "path": "Observation.component.value[x]", "slicing": { "discriminator": [ { "type": "type", "path": "$this" } ], "ordered": false, "rules": "open" } }, { "id": "Observation.component:gene-studied.value[x]:valueCodeableConcept", "path": "Observation.component.value[x]", "sliceName": "valueCodeableConcept", "short": "The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.", "min": 0, "max": "1", "type": [ { "code": "CodeableConcept" } ], "binding": { "strength": "extensible", "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs" } }, { "id": "Observation.component:biomarker-category", "path": "Observation.component", "sliceName": "biomarker-category", "min": 0, "max": "*", "mustSupport": true }, { "id": "Observation.component:biomarker-category.code", "path": "Observation.component.code", "patternCodeableConcept": { "coding": [ { "code": "biomarker-category", "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] } }, { "id": "Observation.component:biomarker-category.value[x]", "path": "Observation.component.value[x]", "type": [ { "code": "CodeableConcept" } ], "binding": { "strength": "preferred", "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-category-vs" } } ] } }
Mapping Datensatz zu FHIR
Datensatz | Erklaerung | FHIR |
---|---|---|
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:
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".
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".
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