PROTECT-CHILD Pediatric Transplant Data Implementation Guide
0.1.0-ci-build -
PROTECT-CHILD Pediatric Transplant Data Implementation Guide
0.1.0-ci-build - ci-build
PROTECT-CHILD Pediatric Transplant Data Implementation Guide
0.1.0-ci-build - ci-build
PROTECT-CHILD Pediatric Transplant Data Implementation Guide, published by Protect Child. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/hl7-eu/protect-child/ and changes regularly. See the Directory of published versions
| Official URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology | Version: 0.1.0-ci-build | |||
| Draft as of 2026-02-09 | Computable Name: Microbiology | |||
Microbiology results related to transplant recipients and/or donors, aligned with the microbiology table.
Usages:
You can also check for usages in the FHIR IG Statistics
Description of Profiles, Differentials, Snapshots and how the different presentations work.
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.identifier.use | Base | required | IdentifierUse | 📍4.0.1 | FHIR Std. |
| Observation.status | Base | required | ObservationStatus | 📍4.0.1 | FHIR Std. |
| Observation.code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources |
contained.contained.empty()
|
| dom-3 | error | Observation | If 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-4 | error | Observation | If 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-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label |
contained.meta.security.empty()
|
| dom-6 | best practice | Observation | A resource should have narrative for robust management |
text.`div`.exists()
|
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both |
extension.exists() != value.exists()
|
| microbiology-ebv-dna-nonnegative | error | Observation.extension:ebv_dna | EBV-DNA value must be zero or positive. |
valueDecimal >= 0
|
| obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present |
dataAbsentReason.empty() or value.empty()
|
| obs-7 | error | Observation | If 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
| Name | Flags | Card. | Type | Description & Constraints Filter:   | ||||
|---|---|---|---|---|---|---|---|---|
  Observation |
C | 0..* | Observation | Measurements and simple assertions Constraints: obs-6, obs-7 | ||||
  id |
Σ | 0..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 | ||||
| language |
0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| 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 | |||||
  Slices for extension |
21..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
   extension:patient_id |
S | 0..1 | Reference(Transplant Recipient) | patient_id – reference to PatientTransplant URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-patient-ref | ||||
| extension:donor_id |
S | 0..1 | Reference(Transplant Donor) | donor_id – reference to Donor URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-donor-ref | ||||
| extension:ebv_dna |
SC | 1..1 | decimal | ebv_dna – EBV nucleic acid test result (float) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-ebv-dna Constraints: microbiology-ebv-dna-nonnegative | ||||
| extension:ebv_igm_anti_ea |
S | 1..1 | boolean | ebv_igm_anti_ea – EBV serology IgM anti-EA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-ebv-igm-anti-ea | ||||
| extension:ebv_igm_anti_vca |
S | 1..1 | boolean | ebv_igm_anti_vca – EBV serology IgM anti-VCA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-ebv-igm-anti-vca | ||||
| extension:ebv_igg_anti_vca |
S | 1..1 | boolean | ebv_igg_anti_vca – EBV serology IgG anti-VCA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-ebv-igg-anti-vca | ||||
| extension:ebv_igg_ebna |
S | 1..1 | boolean | ebv_igg_ebna – EBV serology IgG EBNA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-ebv-igg-ebna | ||||
| extension:cmv_dna |
S | 1..1 | boolean | cmv_dna – Blood CMV-DNA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-cmv-dna | ||||
| extension:cmv_igm |
S | 1..1 | boolean | cmv_igm – CMV serology IgM (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-cmv-igm | ||||
| extension:cmv_igg |
S | 1..1 | boolean | cmv_igg – CMV serology IgG (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-cmv-igg | ||||
| extension:parvovirus_b19_dna |
S | 1..1 | boolean | parvovirus_b19_dna – Blood Parvovirus B19-DNA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-parvovirus-b19-dna | ||||
| extension:parvovirus_b19_dna_igg |
S | 1..1 | boolean | parvovirus_b19_dna_igg – Parvovirus B19 serology IgG (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-parvovirus-b19-dna-igg | ||||
| extension:parvovirus_b19_dna_igm |
S | 1..1 | boolean | parvovirus_b19_dna_igm – Parvovirus B19 serology IgM (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-parvovirus-b19-dna-igm | ||||
| extension:hsv_igg |
S | 1..1 | boolean | hsv_igg – HSV serology IgG (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-hsv-igg | ||||
| extension:hsv_igm |
S | 1..1 | boolean | hsv_igm – HSV serology IgM (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-hsv-igm | ||||
| extension:adenovirus_igg |
S | 1..1 | boolean | adenovirus_igg – Adenovirus serology IgG (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-adenovirus-igg | ||||
| extension:adenovirus_igm |
S | 1..1 | boolean | adenovirus_igm – Adenovirus serology IgM (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-adenovirus-igm | ||||
| extension:vzv_igg |
S | 1..1 | boolean | vzv_igg – VZV serology IgG (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-vzv-igg | ||||
| extension:vzv_igm |
S | 1..1 | boolean | vzv_igm – VZV serology IgM (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-vzv-igm | ||||
| extension:blood_bkv_dna |
S | 1..1 | boolean | blood_bkv_dna – Blood BKV-DNA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-blood-bkv-dna | ||||
| extension:urine_bkv_dna |
S | 1..1 | boolean | urine_bkv_dna – Urine BKV-DNA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-urine-bkv-dna | ||||
| extension:bkv_dna_kidney_biopsy |
S | 1..1 | boolean | bkv_dna_kidney_biopsy – BKV-DNA on kidney biopsy (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-bkv-dna-kidney-biopsy | ||||
 extension:bkv_fish_kidney_biopsy |
S | 1..1 | boolean | bkv_fish_kidney_biopsy – BKV FISH on kidney biopsy (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-bkv-fish-kidney-biopsy | ||||
 modifierExtension |
?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
SΣ | 1..1 | Identifier | microbiology_id – Microbiology ID from the data model | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| use |
?!Σ | 0..1 | code | usual | official | temp | secondary | old (If known) Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known . | ||||
| type |
Σ | 0..1 | CodeableConcept | Description of identifier Binding: Identifier Type Codes (extensible): A coded type for an identifier that can be used to determine which identifier to use for a specific purpose. | ||||
| system |
Σ | 1..1 | uri | The namespace for the identifier value Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/microbiology-id | ||||
| value |
Σ | 1..1 | string | The value that is unique Example General: 123456 | ||||
| period |
Σ | 0..1 | Period | Time period when id is/was valid for use | ||||
  assigner |
Σ | 0..1 | Reference(Organization) | Organization that issued id (may be just text) | ||||
| basedOn |
Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order | ||||
| partOf |
Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) | Part of referenced event | ||||
| status |
?!SΣ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. Required Pattern: final | ||||
| category |
0..* | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| code |
SΣ | 1..1 | CodeableConcept | Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| 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 | ||||
| text |
Σ | 0..1 | string | Plain text representation of the concept Required Pattern: Microbiology panel | ||||
| subject |
SΣ | 0..1 | Reference(Patient | Group | Device | Location) | Optional subject; may be recipient or donor. See patient_id and donor_id extensions for exact linkage. | ||||
| focus |
Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
| 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 | ||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| 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. | |||||
| method |
0..1 | CodeableConcept | How it was done Binding: ObservationMethods (example): Methods for simple observations. | |||||
| specimen |
0..1 | Reference(Specimen) | Specimen used for this observation | |||||
| device |
0..1 | Reference(Device | DeviceMetric) | (Measurement) Device | |||||
| 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(4.0.1) | Low Range, if relevant | ||||
| high |
C | 0..1 | SimpleQuantity(4.0.1) | 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 | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group | ||||
| derivedFrom |
Σ | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from | ||||
 component |
Σ | 0..* | BackboneElement | Component results | ||||
 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 | ||||
| code |
Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| value[x] |
Σ | 0..1 | Actual component result | |||||
| valueQuantity |
Quantity | |||||||
| valueCodeableConcept |
CodeableConcept | |||||||
| valueString |
string | |||||||
| valueBoolean |
boolean | |||||||
| valueInteger |
integer | |||||||
| valueRange |
Range | |||||||
| valueRatio |
Ratio | |||||||
| valueSampledData |
SampledData | |||||||
| valueTime |
time | |||||||
| valueDateTime |
dateTime | |||||||
| valuePeriod |
Period | |||||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation |
0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
 referenceRange |
0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| Documentation for this format | ||||||||
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.language | Base | preferred | Common Languages | 📍4.0.1 | FHIR Std. |
| Observation.identifier.use | Base | required | IdentifierUse | 📍4.0.1 | FHIR Std. |
| Observation.identifier.type | Base | extensible | IdentifierType | 📍4.0.1 | FHIR Std. |
| Observation.status | Base | required | ObservationStatus | 📍4.0.1 | FHIR Std. |
| Observation.category | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std. |
| Observation.code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std. |
| Observation.dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std. |
| Observation.interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std. |
| Observation.bodySite | Base | example | SNOMED CT Body Structures | 📍4.0.1 | FHIR Std. |
| Observation.method | Base | example | Observation Methods | 📍4.0.1 | FHIR Std. |
| Observation.referenceRange.type | Base | preferred | Observation Reference Range Meaning Codes | 📍4.0.1 | FHIR Std. |
| Observation.referenceRange.appliesTo | Base | example | Observation Reference Range Applies To Codes | 📍4.0.1 | FHIR Std. |
| Observation.component.code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std. |
| Observation.component.dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std. |
| Observation.component.interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources |
contained.contained.empty()
|
| dom-3 | error | Observation | If 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-4 | error | Observation | If 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-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label |
contained.meta.security.empty()
|
| dom-6 | best practice | Observation | A resource should have narrative for robust management |
text.`div`.exists()
|
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both |
extension.exists() != value.exists()
|
| microbiology-ebv-dna-nonnegative | error | Observation.extension:ebv_dna | EBV-DNA value must be zero or positive. |
valueDecimal >= 0
|
| obs-3 | error | Observation.referenceRange | Must have at least a low or a high or text |
low.exists() or high.exists() or text.exists()
|
| obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present |
dataAbsentReason.empty() or value.empty()
|
| obs-7 | error | Observation | If 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: 24 elements
Must-Support: 27 elements
Fixed: 1 element
Prohibited: 1 element
Extensions
This structure refers to these extensions:
Key Elements View
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.identifier.use | Base | required | IdentifierUse | 📍4.0.1 | FHIR Std. |
| Observation.status | Base | required | ObservationStatus | 📍4.0.1 | FHIR Std. |
| Observation.code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources |
contained.contained.empty()
|
| dom-3 | error | Observation | If 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-4 | error | Observation | If 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-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label |
contained.meta.security.empty()
|
| dom-6 | best practice | Observation | A resource should have narrative for robust management |
text.`div`.exists()
|
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both |
extension.exists() != value.exists()
|
| microbiology-ebv-dna-nonnegative | error | Observation.extension:ebv_dna | EBV-DNA value must be zero or positive. |
valueDecimal >= 0
|
| obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present |
dataAbsentReason.empty() or value.empty()
|
| obs-7 | error | Observation | If 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
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints Filter: | ||||
|---|---|---|---|---|---|---|---|---|
| Observation |
C | 0..* | Observation | Measurements and simple assertions Constraints: obs-6, obs-7 | ||||
| id |
Σ | 0..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 | ||||
| language |
0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| 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 | |||||
| Slices for extension |
21..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| extension:patient_id |
S | 0..1 | Reference(Transplant Recipient) | patient_id – reference to PatientTransplant URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-patient-ref | ||||
| extension:donor_id |
S | 0..1 | Reference(Transplant Donor) | donor_id – reference to Donor URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-donor-ref | ||||
| extension:ebv_dna |
SC | 1..1 | decimal | ebv_dna – EBV nucleic acid test result (float) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-ebv-dna Constraints: microbiology-ebv-dna-nonnegative | ||||
| extension:ebv_igm_anti_ea |
S | 1..1 | boolean | ebv_igm_anti_ea – EBV serology IgM anti-EA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-ebv-igm-anti-ea | ||||
| extension:ebv_igm_anti_vca |
S | 1..1 | boolean | ebv_igm_anti_vca – EBV serology IgM anti-VCA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-ebv-igm-anti-vca | ||||
| extension:ebv_igg_anti_vca |
S | 1..1 | boolean | ebv_igg_anti_vca – EBV serology IgG anti-VCA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-ebv-igg-anti-vca | ||||
| extension:ebv_igg_ebna |
S | 1..1 | boolean | ebv_igg_ebna – EBV serology IgG EBNA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-ebv-igg-ebna | ||||
| extension:cmv_dna |
S | 1..1 | boolean | cmv_dna – Blood CMV-DNA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-cmv-dna | ||||
| extension:cmv_igm |
S | 1..1 | boolean | cmv_igm – CMV serology IgM (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-cmv-igm | ||||
| extension:cmv_igg |
S | 1..1 | boolean | cmv_igg – CMV serology IgG (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-cmv-igg | ||||
| extension:parvovirus_b19_dna |
S | 1..1 | boolean | parvovirus_b19_dna – Blood Parvovirus B19-DNA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-parvovirus-b19-dna | ||||
| extension:parvovirus_b19_dna_igg |
S | 1..1 | boolean | parvovirus_b19_dna_igg – Parvovirus B19 serology IgG (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-parvovirus-b19-dna-igg | ||||
| extension:parvovirus_b19_dna_igm |
S | 1..1 | boolean | parvovirus_b19_dna_igm – Parvovirus B19 serology IgM (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-parvovirus-b19-dna-igm | ||||
| extension:hsv_igg |
S | 1..1 | boolean | hsv_igg – HSV serology IgG (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-hsv-igg | ||||
| extension:hsv_igm |
S | 1..1 | boolean | hsv_igm – HSV serology IgM (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-hsv-igm | ||||
| extension:adenovirus_igg |
S | 1..1 | boolean | adenovirus_igg – Adenovirus serology IgG (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-adenovirus-igg | ||||
| extension:adenovirus_igm |
S | 1..1 | boolean | adenovirus_igm – Adenovirus serology IgM (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-adenovirus-igm | ||||
| extension:vzv_igg |
S | 1..1 | boolean | vzv_igg – VZV serology IgG (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-vzv-igg | ||||
| extension:vzv_igm |
S | 1..1 | boolean | vzv_igm – VZV serology IgM (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-vzv-igm | ||||
| extension:blood_bkv_dna |
S | 1..1 | boolean | blood_bkv_dna – Blood BKV-DNA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-blood-bkv-dna | ||||
| extension:urine_bkv_dna |
S | 1..1 | boolean | urine_bkv_dna – Urine BKV-DNA (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-urine-bkv-dna | ||||
| extension:bkv_dna_kidney_biopsy |
S | 1..1 | boolean | bkv_dna_kidney_biopsy – BKV-DNA on kidney biopsy (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-bkv-dna-kidney-biopsy | ||||
| extension:bkv_fish_kidney_biopsy |
S | 1..1 | boolean | bkv_fish_kidney_biopsy – BKV FISH on kidney biopsy (false=Negative, true=Positive) URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/microbiology-bkv-fish-kidney-biopsy | ||||
| modifierExtension |
?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
SΣ | 1..1 | Identifier | microbiology_id – Microbiology ID from the data model | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| use |
?!Σ | 0..1 | code | usual | official | temp | secondary | old (If known) Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known . | ||||
| type |
Σ | 0..1 | CodeableConcept | Description of identifier Binding: Identifier Type Codes (extensible): A coded type for an identifier that can be used to determine which identifier to use for a specific purpose. | ||||
| system |
Σ | 1..1 | uri | The namespace for the identifier value Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/microbiology-id | ||||
| value |
Σ | 1..1 | string | The value that is unique Example General: 123456 | ||||
| period |
Σ | 0..1 | Period | Time period when id is/was valid for use | ||||
| assigner |
Σ | 0..1 | Reference(Organization) | Organization that issued id (may be just text) | ||||
| basedOn |
Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order | ||||
| partOf |
Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) | Part of referenced event | ||||
| status |
?!SΣ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. Required Pattern: final | ||||
| category |
0..* | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| code |
SΣ | 1..1 | CodeableConcept | Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| 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 | ||||
| text |
Σ | 0..1 | string | Plain text representation of the concept Required Pattern: Microbiology panel | ||||
| subject |
SΣ | 0..1 | Reference(Patient | Group | Device | Location) | Optional subject; may be recipient or donor. See patient_id and donor_id extensions for exact linkage. | ||||
| focus |
Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
| 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 | ||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| 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. | |||||
| method |
0..1 | CodeableConcept | How it was done Binding: ObservationMethods (example): Methods for simple observations. | |||||
| specimen |
0..1 | Reference(Specimen) | Specimen used for this observation | |||||
| device |
0..1 | Reference(Device | DeviceMetric) | (Measurement) Device | |||||
| 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(4.0.1) | Low Range, if relevant | ||||
| high |
C | 0..1 | SimpleQuantity(4.0.1) | 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 | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group | ||||
| derivedFrom |
Σ | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from | ||||
| component |
Σ | 0..* | BackboneElement | Component results | ||||
| 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 | ||||
| code |
Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| value[x] |
Σ | 0..1 | Actual component result | |||||
| valueQuantity |
Quantity | |||||||
| valueCodeableConcept |
CodeableConcept | |||||||
| valueString |
string | |||||||
| valueBoolean |
boolean | |||||||
| valueInteger |
integer | |||||||
| valueRange |
Range | |||||||
| valueRatio |
Ratio | |||||||
| valueSampledData |
SampledData | |||||||
| valueTime |
time | |||||||
| valueDateTime |
dateTime | |||||||
| valuePeriod |
Period | |||||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation |
0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange |
0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| Documentation for this format | ||||||||
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.language | Base | preferred | Common Languages | 📍4.0.1 | FHIR Std. |
| Observation.identifier.use | Base | required | IdentifierUse | 📍4.0.1 | FHIR Std. |
| Observation.identifier.type | Base | extensible | IdentifierType | 📍4.0.1 | FHIR Std. |
| Observation.status | Base | required | ObservationStatus | 📍4.0.1 | FHIR Std. |
| Observation.category | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std. |
| Observation.code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std. |
| Observation.dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std. |
| Observation.interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std. |
| Observation.bodySite | Base | example | SNOMED CT Body Structures | 📍4.0.1 | FHIR Std. |
| Observation.method | Base | example | Observation Methods | 📍4.0.1 | FHIR Std. |
| Observation.referenceRange.type | Base | preferred | Observation Reference Range Meaning Codes | 📍4.0.1 | FHIR Std. |
| Observation.referenceRange.appliesTo | Base | example | Observation Reference Range Applies To Codes | 📍4.0.1 | FHIR Std. |
| Observation.component.code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std. |
| Observation.component.dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std. |
| Observation.component.interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources |
contained.contained.empty()
|
| dom-3 | error | Observation | If 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-4 | error | Observation | If 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-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label |
contained.meta.security.empty()
|
| dom-6 | best practice | Observation | A resource should have narrative for robust management |
text.`div`.exists()
|
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both |
extension.exists() != value.exists()
|
| microbiology-ebv-dna-nonnegative | error | Observation.extension:ebv_dna | EBV-DNA value must be zero or positive. |
valueDecimal >= 0
|
| obs-3 | error | Observation.referenceRange | Must have at least a low or a high or text |
low.exists() or high.exists() or text.exists()
|
| obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present |
dataAbsentReason.empty() or value.empty()
|
| obs-7 | error | Observation | If 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: 24 elements
Must-Support: 27 elements
Fixed: 1 element
Prohibited: 1 element
Extensions
This structure refers to these extensions:
Other representations of profile: CSV, Excel, Schematron