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: ObservationMicrobiology

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

Introduction

The ObservationMicrobiology profile represents the result information of a microbiology request and is a profile created from the resource Observation. The Resistance results will not be shown using this Observation profile, only the results of other microbiology examinations done on the sample of the patient. 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

The profile ObservationMicrobiology is used for communicating an entry of a result of a microbiology test done by sending a value in the element observation.value. This profile is referenced in the basedOn field of DiagnosticReport FHIR profile. The API can be used to read result information for a specific microbiology test done as a part of a microbiology.

Organization profile used for performer supports requesting PDL hierarchy details as well, it will have the full hierarchy of units related to performer.

COS version Profile version Required COSMIC version Date Description
3.0.0 1.0.0 R8.3.05 May 2022 initial version

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
.. Observation C 0..* Observation Measurements and simple assertions
Constraints: obs-6, obs-7
... 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 registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
... category 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
... code Σ 1..1 CodeableConcept Type of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
... subject Σ 0..1 Reference(Patient) Who and/or what the observation is about
... effective[x] Σ 0..1 Clinically relevant time/time-period for observation
.... effectiveDateTime dateTime
.... effectivePeriod Period
.... effectiveTiming Timing
.... effectiveInstant instant
... hasMember Σ 0..* Reference(Observation) Related resource that belongs to the Observation group

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
From the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
From the FHIR Standard
Observation.codeexampleLOINCCodes(a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
From the FHIR Standard
Observation.component.codeexampleLOINCCodes(a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
From the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA 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()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
: value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from Observation

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation 0..* Observation Measurements and simple assertions
... id 1..1 id Logical id of this artifact
... basedOn 0..* Reference(ServiceRequest) Fulfills plan, proposal or order
... partOf 0..0
... subject 0..1 Reference(Patient) Who and/or what the observation is about
... focus 0..0
... effective[x] 0..1 dateTime, Period, Timing, instant Clinically relevant time/time-period for observation
... dataAbsentReason 0..0
... method 0..0
... device 0..0
... hasMember 0..* Reference(Observation) Related resource that belongs to the Observation group
... derivedFrom 0..0
... component 0..0

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* Observation Measurements and simple assertions
Constraints: obs-6, obs-7
... 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 observation
... basedOn Σ 0..* Reference(ServiceRequest) Fulfills plan, proposal or order
... status ?!Σ 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
... category 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
... code Σ 1..1 CodeableConcept Type of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
... subject Σ 0..1 Reference(Patient) Who and/or what the observation is about
... encounter Σ 0..1 Reference(Encounter) Healthcare event during which this observation is made
... effective[x] Σ 0..1 Clinically relevant time/time-period for observation
.... effectiveDateTime dateTime
.... effectivePeriod Period
.... effectiveTiming Timing
.... effectiveInstant instant
... issued Σ 0..1 instant Date/Time this version was made available
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Who is responsible for the observation
... value[x] ΣC 0..1 Actual result
.... valueQuantity Quantity
.... valueCodeableConcept CodeableConcept
.... valueString string
.... valueBoolean boolean
.... valueInteger integer
.... valueRange Range
.... valueRatio Ratio
.... valueSampledData SampledData
.... valueTime time
.... valueDateTime dateTime
.... valuePeriod Period
... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
... note 0..* Annotation Comments about the observation
... bodySite 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
... specimen 0..1 Reference(Specimen) Specimen used for this observation
... referenceRange C 0..* BackboneElement Provides guide for interpretation
Constraints: obs-3
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... low C 0..1 SimpleQuantity Low Range, if relevant
.... high C 0..1 SimpleQuantity High Range, if relevant
.... type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
.... appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
.... age 0..1 Range Applicable age range, if relevant
.... text 0..1 string Text based reference range in an observation
... hasMember Σ 0..* Reference(Observation) Related resource that belongs to the Observation group

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
Observation.languagepreferredCommonLanguages
http://hl7.org/fhir/ValueSet/languages
From the FHIR Standard
Additional Bindings Purpose
AllLanguages Max Binding
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
From the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
From the FHIR Standard
Observation.codeexampleLOINCCodes(a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
From the FHIR Standard
Observation.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
From the FHIR Standard
Observation.bodySiteexampleSNOMEDCTBodyStructures
http://hl7.org/fhir/ValueSet/body-site
From the FHIR Standard
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
http://hl7.org/fhir/ValueSet/referencerange-meaning
From the FHIR Standard
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
http://hl7.org/fhir/ValueSet/referencerange-appliesto
From the FHIR Standard
Observation.component.codeexampleLOINCCodes(a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
From the FHIR Standard
Observation.component.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
From the FHIR Standard
Observation.component.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
From the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA 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()
obs-3errorObservation.referenceRangeMust have at least a low or a high or text
: low.exists() or high.exists() or text.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
: value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from Observation

Summary

Mandatory: 2 elements
Prohibited: 7 elements

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* Observation Measurements and simple assertions
Constraints: obs-6, obs-7
... 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 registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
... category 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
... code Σ 1..1 CodeableConcept Type of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
... subject Σ 0..1 Reference(Patient) Who and/or what the observation is about
... effective[x] Σ 0..1 Clinically relevant time/time-period for observation
.... effectiveDateTime dateTime
.... effectivePeriod Period
.... effectiveTiming Timing
.... effectiveInstant instant
... hasMember Σ 0..* Reference(Observation) Related resource that belongs to the Observation group

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
From the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
From the FHIR Standard
Observation.codeexampleLOINCCodes(a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
From the FHIR Standard
Observation.component.codeexampleLOINCCodes(a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
From the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA 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()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
: value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

Differential View

This structure is derived from Observation

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation 0..* Observation Measurements and simple assertions
... id 1..1 id Logical id of this artifact
... basedOn 0..* Reference(ServiceRequest) Fulfills plan, proposal or order
... partOf 0..0
... subject 0..1 Reference(Patient) Who and/or what the observation is about
... focus 0..0
... effective[x] 0..1 dateTime, Period, Timing, instant Clinically relevant time/time-period for observation
... dataAbsentReason 0..0
... method 0..0
... device 0..0
... hasMember 0..* Reference(Observation) Related resource that belongs to the Observation group
... derivedFrom 0..0
... component 0..0

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* Observation Measurements and simple assertions
Constraints: obs-6, obs-7
... 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 observation
... basedOn Σ 0..* Reference(ServiceRequest) Fulfills plan, proposal or order
... status ?!Σ 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
... category 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
... code Σ 1..1 CodeableConcept Type of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
... subject Σ 0..1 Reference(Patient) Who and/or what the observation is about
... encounter Σ 0..1 Reference(Encounter) Healthcare event during which this observation is made
... effective[x] Σ 0..1 Clinically relevant time/time-period for observation
.... effectiveDateTime dateTime
.... effectivePeriod Period
.... effectiveTiming Timing
.... effectiveInstant instant
... issued Σ 0..1 instant Date/Time this version was made available
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Who is responsible for the observation
... value[x] ΣC 0..1 Actual result
.... valueQuantity Quantity
.... valueCodeableConcept CodeableConcept
.... valueString string
.... valueBoolean boolean
.... valueInteger integer
.... valueRange Range
.... valueRatio Ratio
.... valueSampledData SampledData
.... valueTime time
.... valueDateTime dateTime
.... valuePeriod Period
... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
... note 0..* Annotation Comments about the observation
... bodySite 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
... specimen 0..1 Reference(Specimen) Specimen used for this observation
... referenceRange C 0..* BackboneElement Provides guide for interpretation
Constraints: obs-3
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... low C 0..1 SimpleQuantity Low Range, if relevant
.... high C 0..1 SimpleQuantity High Range, if relevant
.... type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
.... appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
.... age 0..1 Range Applicable age range, if relevant
.... text 0..1 string Text based reference range in an observation
... hasMember Σ 0..* Reference(Observation) Related resource that belongs to the Observation group

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
Observation.languagepreferredCommonLanguages
http://hl7.org/fhir/ValueSet/languages
From the FHIR Standard
Additional Bindings Purpose
AllLanguages Max Binding
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
From the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
From the FHIR Standard
Observation.codeexampleLOINCCodes(a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
From the FHIR Standard
Observation.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
From the FHIR Standard
Observation.bodySiteexampleSNOMEDCTBodyStructures
http://hl7.org/fhir/ValueSet/body-site
From the FHIR Standard
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
http://hl7.org/fhir/ValueSet/referencerange-meaning
From the FHIR Standard
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
http://hl7.org/fhir/ValueSet/referencerange-appliesto
From the FHIR Standard
Observation.component.codeexampleLOINCCodes(a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
From the FHIR Standard
Observation.component.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
From the FHIR Standard
Observation.component.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
From the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA 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()
obs-3errorObservation.referenceRangeMust have at least a low or a high or text
: low.exists() or high.exists() or text.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
: value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from Observation

Summary

Mandatory: 2 elements
Prohibited: 7 elements

 

Other representations of profile: CSV, Excel, Schematron