description: This profile is used to represent laboratory measurements of human inherent substances such as gene products, antigens and antibodies, and complex chemicals that result from post-translational processing of multi-gene products.
package_name: hl7.fhir.uv.genomics-reporting
derivation: constraint
name: MolecularBiomarker
type: Observation
elements:
  category:
    array: true
    min: 2
    index: 0
    slicing:
      rules: open
      description: Slice based on the category.code pattern
      discriminator:
      - {path: coding, type: pattern}
      min: 2
      slices:
        labCategory:
          match:
            coding: {code: laboratory, system: 'http://terminology.hl7.org/CodeSystem/observation-category'}
          schema:
            _required: true
            index: 1
            elements:
              coding:
                pattern:
                  type: Coding
                  value: {code: laboratory, system: 'http://terminology.hl7.org/CodeSystem/observation-category'}
                index: 2
            required: [coding]
        mbCategory:
          match:
            coding: {code: biomarker-category, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs'}
          schema:
            _required: true
            index: 3
            elements:
              coding:
                pattern:
                  type: Coding
                  value: {code: biomarker-category, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs'}
                index: 4
            required: [coding]
        geCategory:
          match:
            coding: {code: GE, system: 'http://terminology.hl7.org/CodeSystem/v2-0074'}
          schema:
            index: 5
            elements:
              coding:
                pattern:
                  type: Coding
                  value: {code: GE, system: 'http://terminology.hl7.org/CodeSystem/v2-0074'}
                index: 6
            required: [coding]
  code:
    short: Code for the biomarker
    binding: {strength: example, valueSet: 'http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-code-vs'}
    index: 7
  component:
    index: 8
    slicing:
      rules: open
      description: Slice based on the component.code pattern
      discriminator:
      - {path: code, type: pattern}
      min: null
      slices:
        gene-studied:
          match:
            code:
              coding:
              - {code: 48018-6, system: 'http://loinc.org'}
          schema:
            short: Gene Studied
            array: true
            index: 9
            elements:
              code:
                short: 48018-6
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48018-6, system: 'http://loinc.org'}
                index: 10
              value:
                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.
                choices: [valueCodeableConcept]
                index: 12
              valueCodeableConcept: {type: CodeableConcept, 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.', choiceOf: value, index: 13}
            required: [value, valueCodeableConcept]
        biomarker-category:
          match:
            code:
              coding:
              - {code: biomarker-category, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs'}
          schema:
            short: Biomarker Category
            array: true
            index: 14
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: biomarker-category, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs'}
                index: 15
              value:
                short: cell receptor | antigen | protein | immune stain
                choices: [valueCodeableConcept]
                index: 17
              valueCodeableConcept: {type: CodeableConcept, short: cell receptor | antigen | protein | immune stain, choiceOf: value, index: 18}
            required: [value, valueCodeableConcept]
package_version: 3.0.0-ballot
class: profile
kind: resource
url: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker
base: http://hl7.org/fhir/StructureDefinition/Observation
version: 3.0.0-ballot