ISA-to-FHIR Mapping

Tables

ISA JSON object ISA JSON properties FHIR Elements Comments
Investigation ResearchStudy
Investigation @id
Investigation filename
Investigation identifier ResearchStudy.identifier
Investigation title ResearchStudy.title
Investigation description ResearchStudy.description
Investigation submissionDate ResearchStudy.extension:submissionDate.valueDateTime
Investigation publicReleaseDate ResearchStudy.extension:publicReleaseDate.valueDateTime
Investigation ontologySourceReferences Information related to CodeSystems would not be stored centrally in a FHIR resource. Codings would refer to relevant CodeSystems.
Investigation publications ResearchStudy.relatedArtifact
Investigation people ResearchStudy.contact.extension:people.valueReference(Practitioner or PractitionerRole) Changes planned in R5: New element ResearchStudy.associatedParty with References a.o. to Practitioner and PractitionerRole
Investigation studies ResearchStudy.extension:studies.valueReference(ResearchStudy) In FHIR, a smaller study can point to a bigger one with ResearchStudy.partOf
Investigation comments ResearchStudy.note
Study ResearchStudy
Study @id ResearchStudy.id
Study filename
Study identifier ResearchStudy.identifier
Study title ResearchStudy.title
Study description ResearchStudy.description
Study submissionDate ResearchStudy.extension:submissionDate.valueDateTime
Study publicReleaseDate ResearchStudy.extension:publicReleaseDate.valueDateTime
Study publications ResearchStudy.relatedArtifact
Study people ResearchStudy.contact.extension:people.valueReference(Practitioner or PractitionerRole) Changes planned in R5: New element ResearchStudy.associatedParty with References a.o. to Practitioner and PractitionerRole
Study studyDesignDescriptors Several FHIR elements might be suitable, e.g., ResearchStudy.category, ResearchStudy.phase, ResearchStudy.primaryPurposeType, ResearchStudy.focus...
Study protocols ResearchStudy.protocol
Study materials ResearchStudy.extension:materials
Study materials.sources ResearchStudy.extension:materials.extension:sources.valueReference(Specimen)
Study materials.samples ResearchStudy.extension:materials.extension:sources.valueReference(Specimen)
Study materials.otherMaterials ResearchStudy.extension:materials.extension:sources.valueReference(Specimen)
Study processSequence ResearchStudy.protocol
Study assays ResearchStudy.extension:assays.valueReference(Observation)
Study factors ResearchStudy.extension:factors Changes planned in R5: New element ResearchStudy.outcomeMeasure
Study characteristicCategories Data related to material characteristics would be rather stored in a Specimen resource
Study unitCategories Data related to units would be rather stored with a Quantity, or through with the extension https://www.hl7.org/fhir/R4/extension-elementdefinition-allowedunits.html
Study comments ResearchStudy.note
Assay Observation Depending on the type of experiments, other FHIR resources might suit too, such as MolecularSequence.
Assay @id Observation.id
Assay comments Observation.note
Assay filename
Assay measurementType Observation.code
Assay technologyType This BackboneElement would not be necessary in FHIR
Assay technologyType.ontologyAnnotation Observation.method
Assay technologyPlatform Observation.device.resolve().manufacturer and Observation.device.resolve().deviceName
Assay dataFiles Observation.extension:dataFiles.Reference(DocumentReference)
Assay materials Observation.specimen or Observation.extension:additionalspecimen.Reference(Specimen) Changes planned in R5 planned: Possibility to refer to a Specimen or a Group via Observation. Group can includes several Specimen.
Assay materials.samples Observation.specimen or Observation.extension:additionalspecimen.Reference(Specimen)
Assay materials.otherMaterials Observation.specimen or Observation.extension:additionalspecimen.Reference(Specimen)
Assay characteristicCategories Data related to material characteristics would be rather stored in a Specimen resource
Assay unitCategories Data related to units would be rather stored with a Quantity, or through with the extension https://www.hl7.org/fhir/R4/extension-elementdefinition-allowedunits.html
Assay processSequence Observation.extension:processSequence.valueReference(PlanDefinition or ActivityDefinition) Changes planned in R5: Possibility to instantiate an ObservationDefinition via Observation. PlanDefinition can define an ObservationDefinition.
Comment Annotation
Comment @id
Comment name Annotation.extension:filename.valueString
Comment value Annotation.text
Data DocumentReference Depending on the concrete data files and types, other FHIR resources such as Media, ImagingStudy or MolecularSequence might be suitable too
Data @id DocumentReference.id
Data name DocumentReference.content.attachment.title
Data type DocumentReference.category.where(code.memberOf('https://www.nfdi4health.de/fhir/ISA/ValueSet/isa-vs-data-local')
Data comments DocumentReference.extension:comments.valueAnnotation
Factor ResearchStudy.extension:factors Information related to Factor and FactorValues would be stored together in ResearchStudy
Factor @id
Factor factorName ResearchStudy.extension:factors.extension:factorName.valueString
Factor factorType ResearchStudy.extension:factors.extension:factorType.valueCodeableConcept
Factor comments ResearchStudy.extension:factors.extension:comments.valueAnnotation
FactorValue Information related to Factor and FactorValues would be stored together in ResearchStudy
FactorValue @id
FactorValue category
FactorValue value[x] ResearchStudy.extension:factors.extension:factorValue.extension:value.(valueCodeableConcept or valueQuantity)
FactorValue unit ResearchStudy.extension:factors.extension:factorValue.extension:value.valueQuantity.unit
MaterialAttribute MaterialAttribute and MaterialAttributeValue would rather be mapped in combination in a Specimen resource, with the attribute being the name of the FHIR element itself, and the attribute value its associated value (e.g., in form of a CodeableConcept).
MaterialAttribute @id
MaterialAttribute characteristicType
MaterialAttributeValue MaterialAttribute and MaterialAttributeValue would rather be mapped in combination in a Specimen resource, with the attribute being the name of the FHIR element itself, and the attribute value its associated value (e.g., in form of a CodeableConcept).
MaterialAttributeValue @id
MaterialAttributeValue category
MaterialAttributeValue value[x]
MaterialAttributeValue unit
Material Specimen During profiling, differentiation between Samples, Sources and otherMaterials would be necessary.
Material @id Specimen.id
Material name
Material type Specimen.type.where(code.memberOf('https://www.nfdi4health.de/fhir/ISA/ValueSet/isa-vs-material-local'))
Material characteristics In FHIR, this element would store information from MaterialAttribute and MaterialAttributeValue
Material derivesFrom Specimen.parent
OntologyAnnotation CodeableConcept or Coding or Quantity" Data stored directly in the respective FHIR elements in a chosen resource
OntologyAnnotation @id
OntologyAnnotation annotationValue[x] CodeableConcept.text or Coding.display or Quantity.value
OntologyAnnotation termSource CodeableConcept.coding.system or Quantity.system
OntologyAnnotation termAccession CodeableConcept.coding.code or Quantity.code
OntologyAnnotation comments CodeableConcept.extension:comments.valueAnnotation pr Quantity.extension:comments.valueAnnotation
OntologySourceReference CodeSystem In FHIR, Coding, CodeableConcepts, etc. would refer to the relevant CodeSystem via .system
OntologySourceReference comments CodeSystem.extension:comments.where(url='http://hl7.org/fhir/StructureDefinition/codesystem-concept-comments')
OntologySourceReference description CodeSystem.description
OntologySourceReference file CodeSystem.url
OntologySourceReference name CodeSystem.name
OntologySourceReference version CodeSystem.version
Person Practitioner
Person @id Practitioner.id
Person lastName Practitioner.name.family
Person firstName Practitioner.name.given
Person midInitials Practitioner.name.given
Person email PractitionerRole.telecom.where(system='email').value
Person phone PractitionerRole.telecom.where(system='phone').value
Person fax PractitionerRole.telecom.where(system='fax').value
Person address PractitionerRole.location.resolve().address
Person affiliation PractionerRole.organization
Person roles PractitionerRole.code
Person comments Practitioner.extension:comments.valueAnnotation
ProcessParameterValue Information related to ProtocolParameter, and ProcessParameterValue would be stored in a PlanDefinition or ActivityDefinition resource in FHIR
ProcessParameterValue category
ProcessParameterValue value[x]
ProcessParameterValue unit
Process PlanDefinition Depending on the type of process, more specific FHIR elements might fit. For example, information related to specimen collection and processing activities should rather be stored in Specimen.collection and Specimen.processing
Process @id PlanDefinition.id
Process name PlanDefinition.title
Process executesProtocol PlanDefinition.action.definition[x].valueReference(PlanDefinition)
Process parameterValues PlanDefinition.action.code or PlanDefinition.action.extension:quantity.valueQuantity
Process performer Observation.performer.valueReference(Practitioner or PractitionerRole) PlanDefinition specifies for example which type of person should conduct the process, but not the actual person that has performed the process. Depending on the type of Process, further FHIR resources and elements might be suitable: e.g., Specimen.collection.collector to define the Practitioner that collected the Specimen.
Process date Observation.effectiveDateTime PlanDefinition specifies for example when a process should take place but not when it actually happened. Depending on the type of Process, further FHIR resources and elements might be suitable: e.g., Specimen.collection.date to define when the Specimen collection happened.
Process previousProcess PlanDefinition.action.definition[x] or PlanDefinition.action.relatedAction
Process nextProcess PlanDefinition.action.definition[x] or PlanDefinition.action.relatedAction
Process inputs PlanDefinition.input
Process outputs PlanDefinition.output
Process comments PlanDefinition.extension:comments.valueAnnotation
ProtocolParameter Information related to ProtocolParameter, and ProcessParameterValue would be stored in a PlanDefinition or ActivityDefinition resource in FHIR
ProtocolParameter @id
ProtocolParameter parameterName
Protocol PlanDefinition
Protocol @id PlanDefinition.id
Protocol comments PlanDefinition.extension:comments.valueAnnotation
Protocol name PlanDefinition.title
Protocol protocolType PlanDefinition.type
Protocol description PlanDefinition.description
Protocol uri PlanDefinition.url
Protocol version PlanDefinition.version
Protocol parameters PlanDefinition.action.code or PlanDefinition.action.extension:quantity.valueQuantity
Protocol components PlanDefinition.action.participant
Protocol components.componentName PlanDefinition.action.participant.extension:componentName.valueString
Protocol components.componentType PlanDefinition.action.participant.extension:componentType.valueCodeableConcept
Publication RelatedArtifact.where(type='citation') Changes planned in R5: Better coverage through the new resource Citation
Publication comments RelatedArtifact.extension:comments.valueAnnotation
Publication pubMedID RelatedArtifact.url
Publication doi RelatedArtifact.url
Publication authorList RelatedArtifact.citation
Publication title RelatedArtifact.citation
Publication status RelatedArtifact.extension:status.valueCodeableConcept
Sample Specimen During profiling, differentiation between Samples, Sources and otherMaterials would be necessary.
Sample @id Specimen.id
Sample name
Sample characteristics In FHIR, this element would store information from MaterialAttribute and MaterialAttributeValue
Sample factorValues Specimen.extension:factorValues.valueReference(ResearchStudy).resolve().extension:factors
Source derivesFrom Specimen.parent
Source Specimen During profiling, differentiation between Samples, Sources and otherMaterials would be necessary.
Source @id Specimen.id
Source name
Source characteristics In FHIR, this element would store information from MaterialAttribute and MaterialAttributeValue