1.0.0 - release

CambioOpenServicesIG - Local Development build (v1.0.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Resource Profile: DiagnosticReportMicrobiology

Official URL: https://fhir.cambio.se/StructureDefinition/DiagnosticReportMicrobiology Version: 1.0.0
Active as of 2025-10-27 Computable Name: DiagnosticReportMicrobiology

Introduction

The DiagnosticReportMicrobiology profile is used for retrieving data about a complete microbiology report for a patient end to end starting from request. This profile is based on the FHIR resource DiagnosticReport.This profile is derived from a core profile created for DiagnosticReport named DiagnosticReportCore. The data available from COSMIC to this profile is only starting from R8.3.03 COSMIC release, information created before this release cannot be taken from this API.

Intended Use

This profile is created as the main profile for the exposing information related to Microbiology report.This profile is based on the core DiagnosticReport profile that is defined for exposing all types of report based resources.

The intended use for reading data with this API is in first hand that the API is applied for direct access and should not be used to transfer data between caregivers. If it should be used for "data copying" between care providers, patient consent must be handled outside the API.

Specific Rules and Limitations

Type Description
Rule External user should only be the patient that has the Microbiology report. E.g. A healthcare professional is not the intended user of the API.
Rule The consumer of the API is responsible for making sure data retrieved is filtered in compliance with laws and regulations prior to presenting it to any end-users.
Rule For reading diagnostic reports, the external system needs to be able to evaluate PDL. This means whether the information can be displayed for a healthcare professional with a specific assignment. PDL data needed (HSA care unit and HSA care provider) is retrieved by including the organization referenced from DiagnosticReport.performer.OrganizationSEVendorLite.

Versions

COS version Profile version Required COSMIC version Date Description
3.0.0 1.0.0 R8.3.05 May 2022 initial version, support for GET

Statuses

FHIR status Status in COSMIC
PRELIMINARY PRELIMINARY
ADDITIONAL APPENDED
FINAL FINAL
Other UNKNOWN

APIs & Supported Operations

HTTP Method Description
GET Support for retrieving DiagnosticReport by report ID.

Search Parameters

Parameter Format Mandatory Comment
_profile string No  
patient reference Yes The subject that the observation is about (if patient). The reference can be a literal reference ex: subject=1 or a Business identifier as well. Ex: subject.identifier=urn:oid:1.2.752.129.2.1.3.1|20200109-6078
date date (range) Yes (to date is optional) Date format YYYY-MM-DDThh:mm:ss+zz:zz

Supported Queries

  1. GET [baseURL]/DiagnosticReport/[id] (Read)
  2. GET [baseURL]/DiagnosticReport/_search?patient=[]&date=[] (Search)
  3. GET [baseURL]/DiagnosticReport/_search?patient=[]&date=[]&_include=[] (Search)

Supported _include params

The following _include parameters are supported:

  1. patient
  2. performer
  3. based-on
  4. date

Usages:

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport 0..* DiagnosticReportCore A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... id Σ 1..1 id Logical id of this artifact
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... status ?!Σ 1..1 code preliminary | final | appended | unknown
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports.
... performer Σ 0..* Reference(Practitioner | Organization) Responsible Diagnostic Service
... resultsInterpreter Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Primary result interpreter

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
DiagnosticReport.statusrequiredDiagnosticReportStatus
http://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1
From the FHIR Standard
DiagnosticReport.codepreferredLOINCDiagnosticReportCodes(a valid code from LOINC)
http://hl7.org/fhir/ValueSet/report-codes
From the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorDiagnosticReportIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorDiagnosticReportIf the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource
: contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4errorDiagnosticReportIf a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
: contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5errorDiagnosticReportIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceDiagnosticReportA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

This structure is derived from DiagnosticReportCore

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport 0..* DiagnosticReportCore A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... id 1..1 id Logical id of this artifact
... basedOn 1..1 Reference(ServiceRequest) What was requested
... status 1..1 code preliminary | final | appended | unknown
.... coding
..... code 0..1 code Symbol in syntax defined by the system
Fixed Value: MB
... code
.... coding
..... system 0..1 uri Identity of the terminology system
Fixed Value: http://snomed.info/sct
..... code 0..1 code Symbol in syntax defined by the system
Fixed Value: 4341000179107
... effective[x] 0..0
... performer 0..* Reference(Practitioner | Organization) Responsible Diagnostic Service
... resultsInterpreter 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Primary result interpreter
... imagingStudy 0..0
... conclusion 0..0
... conclusionCode 0..0

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport 0..* DiagnosticReportCore A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... id Σ 1..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... extension 0..* Extension Additional content defined by implementations
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Business identifier for report
... basedOn 1..1 Reference(ServiceRequest) What was requested
... status ?!Σ 1..1 code preliminary | final | appended | unknown
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.
... category Σ 0..* CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
.... coding Σ 0..* Coding Code defined by a terminology system
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... system Σ 0..1 uri Identity of the terminology system
..... version Σ 0..1 string Version of the system - if relevant
..... code Σ 0..1 code Symbol in syntax defined by the system
Fixed Value: MB
..... display Σ 0..1 string Representation defined by the system
..... userSelected Σ 0..1 boolean If this coding was chosen directly by the user
.... text Σ 0..1 string Plain text representation of the concept
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports.
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
.... coding Σ 0..* Coding Code defined by a terminology system
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... system Σ 0..1 uri Identity of the terminology system
Fixed Value: http://snomed.info/sct
..... version Σ 0..1 string Version of the system - if relevant
..... code Σ 0..1 code Symbol in syntax defined by the system
Fixed Value: 4341000179107
..... display Σ 0..1 string Representation defined by the system
..... userSelected Σ 0..1 boolean If this coding was chosen directly by the user
.... text Σ 0..1 string Plain text representation of the concept
... subject Σ 0..1 Reference(Patient | Group | Device | Location) The subject of the report - usually, but not always, the patient
... encounter Σ 0..1 Reference(Encounter) Health care event when test ordered
... issued Σ 0..1 instant DateTime this version was made
... performer Σ 0..* Reference(Practitioner | Organization) Responsible Diagnostic Service
... resultsInterpreter Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Primary result interpreter
... specimen 0..* Reference(Specimen) Specimens this report is based on
... result 0..* Reference(Observation) Observations

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
DiagnosticReport.languagepreferredCommonLanguages
http://hl7.org/fhir/ValueSet/languages
From the FHIR Standard
Additional Bindings Purpose
AllLanguages Max Binding
DiagnosticReport.statusrequiredDiagnosticReportStatus
http://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1
From the FHIR Standard
DiagnosticReport.categoryexampleDiagnosticServiceSectionCodes
http://hl7.org/fhir/ValueSet/diagnostic-service-sections
From the FHIR Standard
DiagnosticReport.codepreferredLOINCDiagnosticReportCodes(a valid code from LOINC)
http://hl7.org/fhir/ValueSet/report-codes
From the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorDiagnosticReportIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorDiagnosticReportIf the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource
: contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4errorDiagnosticReportIf a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
: contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5errorDiagnosticReportIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceDiagnosticReportA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

This structure is derived from DiagnosticReportCore

Summary

Mandatory: 2 elements
Fixed: 3 elements
Prohibited: 4 elements

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport 0..* DiagnosticReportCore A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... id Σ 1..1 id Logical id of this artifact
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... status ?!Σ 1..1 code preliminary | final | appended | unknown
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports.
... performer Σ 0..* Reference(Practitioner | Organization) Responsible Diagnostic Service
... resultsInterpreter Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Primary result interpreter

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
DiagnosticReport.statusrequiredDiagnosticReportStatus
http://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1
From the FHIR Standard
DiagnosticReport.codepreferredLOINCDiagnosticReportCodes(a valid code from LOINC)
http://hl7.org/fhir/ValueSet/report-codes
From the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorDiagnosticReportIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorDiagnosticReportIf the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource
: contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4errorDiagnosticReportIf a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
: contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5errorDiagnosticReportIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceDiagnosticReportA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

Differential View

This structure is derived from DiagnosticReportCore

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport 0..* DiagnosticReportCore A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... id 1..1 id Logical id of this artifact
... basedOn 1..1 Reference(ServiceRequest) What was requested
... status 1..1 code preliminary | final | appended | unknown
.... coding
..... code 0..1 code Symbol in syntax defined by the system
Fixed Value: MB
... code
.... coding
..... system 0..1 uri Identity of the terminology system
Fixed Value: http://snomed.info/sct
..... code 0..1 code Symbol in syntax defined by the system
Fixed Value: 4341000179107
... effective[x] 0..0
... performer 0..* Reference(Practitioner | Organization) Responsible Diagnostic Service
... resultsInterpreter 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Primary result interpreter
... imagingStudy 0..0
... conclusion 0..0
... conclusionCode 0..0

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport 0..* DiagnosticReportCore A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... id Σ 1..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... extension 0..* Extension Additional content defined by implementations
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Business identifier for report
... basedOn 1..1 Reference(ServiceRequest) What was requested
... status ?!Σ 1..1 code preliminary | final | appended | unknown
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.
... category Σ 0..* CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
.... coding Σ 0..* Coding Code defined by a terminology system
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... system Σ 0..1 uri Identity of the terminology system
..... version Σ 0..1 string Version of the system - if relevant
..... code Σ 0..1 code Symbol in syntax defined by the system
Fixed Value: MB
..... display Σ 0..1 string Representation defined by the system
..... userSelected Σ 0..1 boolean If this coding was chosen directly by the user
.... text Σ 0..1 string Plain text representation of the concept
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports.
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
.... coding Σ 0..* Coding Code defined by a terminology system
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... system Σ 0..1 uri Identity of the terminology system
Fixed Value: http://snomed.info/sct
..... version Σ 0..1 string Version of the system - if relevant
..... code Σ 0..1 code Symbol in syntax defined by the system
Fixed Value: 4341000179107
..... display Σ 0..1 string Representation defined by the system
..... userSelected Σ 0..1 boolean If this coding was chosen directly by the user
.... text Σ 0..1 string Plain text representation of the concept
... subject Σ 0..1 Reference(Patient | Group | Device | Location) The subject of the report - usually, but not always, the patient
... encounter Σ 0..1 Reference(Encounter) Health care event when test ordered
... issued Σ 0..1 instant DateTime this version was made
... performer Σ 0..* Reference(Practitioner | Organization) Responsible Diagnostic Service
... resultsInterpreter Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Primary result interpreter
... specimen 0..* Reference(Specimen) Specimens this report is based on
... result 0..* Reference(Observation) Observations

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
DiagnosticReport.languagepreferredCommonLanguages
http://hl7.org/fhir/ValueSet/languages
From the FHIR Standard
Additional Bindings Purpose
AllLanguages Max Binding
DiagnosticReport.statusrequiredDiagnosticReportStatus
http://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1
From the FHIR Standard
DiagnosticReport.categoryexampleDiagnosticServiceSectionCodes
http://hl7.org/fhir/ValueSet/diagnostic-service-sections
From the FHIR Standard
DiagnosticReport.codepreferredLOINCDiagnosticReportCodes(a valid code from LOINC)
http://hl7.org/fhir/ValueSet/report-codes
From the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorDiagnosticReportIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorDiagnosticReportIf the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource
: contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4errorDiagnosticReportIf a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
: contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5errorDiagnosticReportIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceDiagnosticReportA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

This structure is derived from DiagnosticReportCore

Summary

Mandatory: 2 elements
Fixed: 3 elements
Prohibited: 4 elements

 

Other representations of profile: CSV, Excel, Schematron