Phenomics Exchange for Research and Diagnostics
0.1.0 - ci-build
Phenomics Exchange for Research and Diagnostics
0.1.0 - ci-build
Phenomics Exchange for Research and Diagnostics, published by HL7 International / Clinical Interoperability Council. This guide is not an authorized publication; it is the continuous build for version 0.1.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/phenomics-exchange-ig/ and changes regularly. See the Directory of published versions
| Official URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Biosample | Version: 0.1.0 | |||
| Draft as of 2021-06-08 | Computable Name: Biosample | |||
Copyright/Legal: Global Alliance for Genomics and Health |
||||
A unit of biological material from which the substrate molecules (e.g. genomic DNA, RNA, proteins) for molecular analyses (e.g. sequencing, array hybridisation, mass-spectrometry) are extracted.
In the phenopacket-schema, an Individual can have zero to many Biosamples. A Biosample refers to a unit of biological material from which the substrate molecules (e.g. genomic DNA, RNA, proteins) for molecular analyses (e.g. sequencing, array hybridisation, mass-spectrometry) are extracted. Examples would be a tissue biopsy, a single cell from a culture for single cell genome sequencing or a protein fraction from a gradient centrifugation. Several instances (e.g. technical replicates) or types of experiments (e.g. genomic array as well as RNA-seq experiments) may refer to the same Biosample.
In the GA4GH phenopacket, the id element is a required string identifier. This corresponds to the identifier element of Specimen (this profile specifies this field to be required).
In the GA4GH phenopacket, the individual_id is a string identifier corresponding to the patient from whom the Biosample is derived. Software to transform FHIR code to GA4GH phenopacket code should generally extract an individual id from the subject field of the Specimen. This IG
constraints subject to be a Patient. The identifier field from the Patient object should be used for the individual_id. If the former is not available, implementers can omit the individual_id or set it to another value that is appropriate for the application.
In the GA4GH phenopacket, the derived_from_id is a string identifier of the biosample from which the current biosample was derived. For instance, a given patient may have one Biosample with id example.1 representing a biopsy. We can choose to represent an RNA sample derived
from the biopsy as a separate Biosample object and would set derived_from_id = example.1`. This feature is intended to serve the needs of biobanks and we choose not to represent it explicitly in the FHIR IG.
In the GA4GH phenopacket, the description is a string with arbitrary text. This string should be initialized with the contents of the note element of the Specimen.
In the GA4GH phenopacket, the sampled_tissue is an optional OntologyClass that denotes the tissue from which the sample was taken. It should be initialized from the collection.bodySite field, if available.
In the GA4GH phenopacket, the sample_type is an optional OntologyClass that denotes the type of material, e.g., RNA, DNA, Cultured cells. If available, this field should be initialized based on infomration from the
collection and processing fields of the FHIR Specimen.
In the GA4GH phenopacket, phenotypic_features and measurement_value represent PhenotypeFeatures or Measurements that pertain specifically to the Biosample. In FHIR, we represent this using the corresponding fields of the upper level Phenopacket but require these to reference the id of this Biospecimen. Software for transforming FHIR to GA4GH Phenopackets should place such PhenotypeFeatures or Measurements in the Biosample.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from Specimen
| Path | Conformance | ValueSet | URI |
| Specimen.status | required | SpecimenStatushttp://hl7.org/fhir/ValueSet/specimen-status|4.0.1from the FHIR Standard | |
| Specimen.type | example | Hl7VSSpecimenTypehttp://terminology.hl7.org/ValueSet/v2-0487 | |
| Specimen.collection.bodySite | example | SNOMEDCTBodyStructureshttp://hl7.org/fhir/ValueSet/body-sitefrom the FHIR Standard | |
| Specimen.processing.procedure | example | SpecimenProcessingProcedurehttp://hl7.org/fhir/ValueSet/specimen-processing-procedurefrom the FHIR Standard |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Specimen | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Specimen | 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 | Specimen | 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 | Specimen | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Specimen | 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() |
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
  Specimen |
0..* | Specimen | Sample for analysis | |||||
  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 | |||||
| contained |
0..* | Resource | Contained, inline Resources | |||||
  Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
   Taxonomy |
S | 0..1 | CodeableConcept | Taxonomy URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Taxonomy Binding: Taxonomy (required) | ||||
| HistologicalDiagnosis |
S | 0..* | CodeableConcept | Histological Diagnosis URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/HistologicalDiagnosis Binding: HistologicalDiagnosis (example) | ||||
| TumorProgression |
S | 0..1 | CodeableConcept | Tumor Progression URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/TumorProgression Binding: Tumor Progression (example) | ||||
| TumorGrade |
S | 0..* | CodeableConcept | Tumor Grade URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/TumorGrade Binding: Tumor Grade (example) | ||||
| PathologicalStage |
S | 0..* | CodeableConcept | Pathological Tumor Stage URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PathologicalStage Binding: Tumor Stage (example) | ||||
| PathologicalTnmFinding |
S | 0..* | CodeableConcept | Pathological TNM Finding URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PathologicalTnmFinding Binding: Tumor Stage (example) | ||||
| DiagnosticMarker |
S | 0..* | CodeableConcept | Diagnostic Marker URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/DiagnosticMarker Binding: Diagnostic Marker (example) | ||||
 MaterialSample |
S | 0..1 | CodeableConcept | Material Sample URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/MaterialSample | ||||
 modifierExtension |
?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
SΣ | 1..1 | Identifier | Corresponds to id (GA4GH), i.e., a specimen identifier | ||||
| accessionIdentifier |
Σ | 0..1 | Identifier | Identifier assigned by the lab | ||||
| status |
?!Σ | 0..1 | code | available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen. | ||||
| type |
SΣ | 0..1 | CodeableConcept | Corresponds to sample_type (GA4GH) Binding: hl7VS-specimenType (example): The type of the specimen. | ||||
 subject |
SΣ | 0..1 | Reference(Patient) | Patient.identifier corresponds to individual_id (GA4GH) | ||||
| receivedTime |
Σ | 0..1 | dateTime | The time when specimen was received for processing | ||||
| parent |
0..* | Reference(Specimen) | Specimen from which this specimen originated | |||||
| request |
0..* | Reference(ServiceRequest) | Why the specimen was collected | |||||
| collection |
0..1 | BackboneElement | Collection details | |||||
| 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 | ||||
| collector |
Σ | 0..1 | Reference(Practitioner | PractitionerRole) | Who collected the specimen | ||||
 collected[x] |
SΣ | 0..1 | Corresponds to time_of_collection (GA4GH) | |||||
| collectedDateTime |
dateTime | |||||||
 collectedPeriod |
Period | |||||||
| duration |
Σ | 0..1 | Duration | How long it took to collect specimen | ||||
| quantity |
0..1 | SimpleQuantity | The quantity of specimen collected | |||||
| method |
0..1 | CodeableConcept | Technique used to perform collection Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure. | |||||
| bodySite |
S | 0..1 | CodeableConcept | Anatomical collection site. Corresponds to sampled_tissue (GA4GH) Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | ||||
 fastingStatus[x] |
Σ | 0..1 | Whether or how long patient abstained from food and/or drink Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient. | |||||
 fastingStatusCodeableConcept |
CodeableConcept | |||||||
| fastingStatusDuration |
Duration | |||||||
| processing |
0..* | BackboneElement | Processing and processing step details | |||||
| 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 | ||||
| description |
0..1 | string | Textual description of procedure | |||||
| procedure |
S | 0..1 | CodeableConcept | Corresponds to procedure (GA4GH) Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen. | ||||
| additive |
0..* | Reference(Substance) | Material used in the processing step | |||||
| time[x] |
0..1 | Date and time of specimen processing | ||||||
| timeDateTime |
dateTime | |||||||
| timePeriod |
Period | |||||||
| container |
0..* | BackboneElement | Direct container of specimen (tube/slide, etc.) | |||||
| 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 | ||||
| identifier |
Σ | 0..* | Identifier | Id for the container | ||||
| description |
0..1 | string | Textual description of the container | |||||
| type |
0..1 | CodeableConcept | Kind of container directly associated with specimen Binding: SpecimenContainerType (example): Type of specimen container. | |||||
| capacity |
0..1 | SimpleQuantity | Container volume or size | |||||
| specimenQuantity |
0..1 | SimpleQuantity | Quantity of specimen within container | |||||
| additive[x] |
0..1 | Additive associated with container Binding: hl7VS-additivePreservative (example): Substance added to specimen container. | ||||||
| additiveCodeableConcept |
CodeableConcept | |||||||
| additiveReference |
Reference(Substance) | |||||||
| condition |
Σ | 0..* | CodeableConcept | State of the specimen Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen. | ||||
| note |
S | 0..* | Annotation | Corresponds to description (GA4GH) | ||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet | URI | |||
| Specimen.language | preferred | CommonLanguages
http://hl7.org/fhir/ValueSet/languagesfrom the FHIR Standard | ||||
| Specimen.status | required | SpecimenStatushttp://hl7.org/fhir/ValueSet/specimen-status|4.0.1from the FHIR Standard | ||||
| Specimen.type | example | Hl7VSSpecimenTypehttp://terminology.hl7.org/ValueSet/v2-0487 | ||||
| Specimen.collection.method | example | FHIRSpecimenCollectionMethodhttp://hl7.org/fhir/ValueSet/specimen-collection-methodfrom the FHIR Standard | ||||
| Specimen.collection.bodySite | example | SNOMEDCTBodyStructureshttp://hl7.org/fhir/ValueSet/body-sitefrom the FHIR Standard | ||||
| Specimen.collection.fastingStatus[x] | extensible | Hl7VSRelevantClincialInformationhttp://terminology.hl7.org/ValueSet/v2-0916 | ||||
| Specimen.processing.procedure | example | SpecimenProcessingProcedurehttp://hl7.org/fhir/ValueSet/specimen-processing-procedurefrom the FHIR Standard | ||||
| Specimen.container.type | example | SpecimenContainerTypehttp://hl7.org/fhir/ValueSet/specimen-container-typefrom the FHIR Standard | ||||
| Specimen.container.additive[x] | example | Hl7VSAdditivePreservativehttp://terminology.hl7.org/ValueSet/v2-0371 | ||||
| Specimen.condition | extensible | Hl7VSSpecimenConditionhttp://terminology.hl7.org/ValueSet/v2-0493 |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Specimen | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Specimen | 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 | Specimen | 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 | Specimen | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Specimen | 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() |
This structure is derived from Specimen
Summary
Mandatory: 1 element
Must-Support: 15 elements
Extensions
This structure refers to these extensions:
Differential View
This structure is derived from Specimen
Key Elements View
| Path | Conformance | ValueSet | URI |
| Specimen.status | required | SpecimenStatushttp://hl7.org/fhir/ValueSet/specimen-status|4.0.1from the FHIR Standard | |
| Specimen.type | example | Hl7VSSpecimenTypehttp://terminology.hl7.org/ValueSet/v2-0487 | |
| Specimen.collection.bodySite | example | SNOMEDCTBodyStructureshttp://hl7.org/fhir/ValueSet/body-sitefrom the FHIR Standard | |
| Specimen.processing.procedure | example | SpecimenProcessingProcedurehttp://hl7.org/fhir/ValueSet/specimen-processing-procedurefrom the FHIR Standard |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Specimen | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Specimen | 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 | Specimen | 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 | Specimen | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Specimen | 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() |
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| Specimen |
0..* | Specimen | Sample for analysis | |||||
| 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 | |||||
| contained |
0..* | Resource | Contained, inline Resources | |||||
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| Taxonomy |
S | 0..1 | CodeableConcept | Taxonomy URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Taxonomy Binding: Taxonomy (required) | ||||
| HistologicalDiagnosis |
S | 0..* | CodeableConcept | Histological Diagnosis URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/HistologicalDiagnosis Binding: HistologicalDiagnosis (example) | ||||
| TumorProgression |
S | 0..1 | CodeableConcept | Tumor Progression URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/TumorProgression Binding: Tumor Progression (example) | ||||
| TumorGrade |
S | 0..* | CodeableConcept | Tumor Grade URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/TumorGrade Binding: Tumor Grade (example) | ||||
| PathologicalStage |
S | 0..* | CodeableConcept | Pathological Tumor Stage URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PathologicalStage Binding: Tumor Stage (example) | ||||
| PathologicalTnmFinding |
S | 0..* | CodeableConcept | Pathological TNM Finding URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PathologicalTnmFinding Binding: Tumor Stage (example) | ||||
| DiagnosticMarker |
S | 0..* | CodeableConcept | Diagnostic Marker URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/DiagnosticMarker Binding: Diagnostic Marker (example) | ||||
| MaterialSample |
S | 0..1 | CodeableConcept | Material Sample URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/MaterialSample | ||||
| modifierExtension |
?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
SΣ | 1..1 | Identifier | Corresponds to id (GA4GH), i.e., a specimen identifier | ||||
| accessionIdentifier |
Σ | 0..1 | Identifier | Identifier assigned by the lab | ||||
| status |
?!Σ | 0..1 | code | available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen. | ||||
| type |
SΣ | 0..1 | CodeableConcept | Corresponds to sample_type (GA4GH) Binding: hl7VS-specimenType (example): The type of the specimen. | ||||
| subject |
SΣ | 0..1 | Reference(Patient) | Patient.identifier corresponds to individual_id (GA4GH) | ||||
| receivedTime |
Σ | 0..1 | dateTime | The time when specimen was received for processing | ||||
| parent |
0..* | Reference(Specimen) | Specimen from which this specimen originated | |||||
| request |
0..* | Reference(ServiceRequest) | Why the specimen was collected | |||||
| collection |
0..1 | BackboneElement | Collection details | |||||
| 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 | ||||
| collector |
Σ | 0..1 | Reference(Practitioner | PractitionerRole) | Who collected the specimen | ||||
| collected[x] |
SΣ | 0..1 | Corresponds to time_of_collection (GA4GH) | |||||
| collectedDateTime |
dateTime | |||||||
| collectedPeriod |
Period | |||||||
| duration |
Σ | 0..1 | Duration | How long it took to collect specimen | ||||
| quantity |
0..1 | SimpleQuantity | The quantity of specimen collected | |||||
| method |
0..1 | CodeableConcept | Technique used to perform collection Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure. | |||||
| bodySite |
S | 0..1 | CodeableConcept | Anatomical collection site. Corresponds to sampled_tissue (GA4GH) Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | ||||
| fastingStatus[x] |
Σ | 0..1 | Whether or how long patient abstained from food and/or drink Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient. | |||||
| fastingStatusCodeableConcept |
CodeableConcept | |||||||
| fastingStatusDuration |
Duration | |||||||
| processing |
0..* | BackboneElement | Processing and processing step details | |||||
| 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 | ||||
| description |
0..1 | string | Textual description of procedure | |||||
| procedure |
S | 0..1 | CodeableConcept | Corresponds to procedure (GA4GH) Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen. | ||||
| additive |
0..* | Reference(Substance) | Material used in the processing step | |||||
| time[x] |
0..1 | Date and time of specimen processing | ||||||
| timeDateTime |
dateTime | |||||||
| timePeriod |
Period | |||||||
| container |
0..* | BackboneElement | Direct container of specimen (tube/slide, etc.) | |||||
| 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 | ||||
| identifier |
Σ | 0..* | Identifier | Id for the container | ||||
| description |
0..1 | string | Textual description of the container | |||||
| type |
0..1 | CodeableConcept | Kind of container directly associated with specimen Binding: SpecimenContainerType (example): Type of specimen container. | |||||
| capacity |
0..1 | SimpleQuantity | Container volume or size | |||||
| specimenQuantity |
0..1 | SimpleQuantity | Quantity of specimen within container | |||||
| additive[x] |
0..1 | Additive associated with container Binding: hl7VS-additivePreservative (example): Substance added to specimen container. | ||||||
| additiveCodeableConcept |
CodeableConcept | |||||||
| additiveReference |
Reference(Substance) | |||||||
| condition |
Σ | 0..* | CodeableConcept | State of the specimen Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen. | ||||
| note |
S | 0..* | Annotation | Corresponds to description (GA4GH) | ||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet | URI | |||
| Specimen.language | preferred | CommonLanguages
http://hl7.org/fhir/ValueSet/languagesfrom the FHIR Standard | ||||
| Specimen.status | required | SpecimenStatushttp://hl7.org/fhir/ValueSet/specimen-status|4.0.1from the FHIR Standard | ||||
| Specimen.type | example | Hl7VSSpecimenTypehttp://terminology.hl7.org/ValueSet/v2-0487 | ||||
| Specimen.collection.method | example | FHIRSpecimenCollectionMethodhttp://hl7.org/fhir/ValueSet/specimen-collection-methodfrom the FHIR Standard | ||||
| Specimen.collection.bodySite | example | SNOMEDCTBodyStructureshttp://hl7.org/fhir/ValueSet/body-sitefrom the FHIR Standard | ||||
| Specimen.collection.fastingStatus[x] | extensible | Hl7VSRelevantClincialInformationhttp://terminology.hl7.org/ValueSet/v2-0916 | ||||
| Specimen.processing.procedure | example | SpecimenProcessingProcedurehttp://hl7.org/fhir/ValueSet/specimen-processing-procedurefrom the FHIR Standard | ||||
| Specimen.container.type | example | SpecimenContainerTypehttp://hl7.org/fhir/ValueSet/specimen-container-typefrom the FHIR Standard | ||||
| Specimen.container.additive[x] | example | Hl7VSAdditivePreservativehttp://terminology.hl7.org/ValueSet/v2-0371 | ||||
| Specimen.condition | extensible | Hl7VSSpecimenConditionhttp://terminology.hl7.org/ValueSet/v2-0493 |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Specimen | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Specimen | 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 | Specimen | 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 | Specimen | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Specimen | 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() |
This structure is derived from Specimen
Summary
Mandatory: 1 element
Must-Support: 15 elements
Extensions
This structure refers to these extensions:
Other representations of profile: CSV, Excel, Schematron
IG © 2021+ HL7 International / Clinical Interoperability Council. Package hl7.fhir.uv.phenomics-exchange#0.1.0 based on FHIR 4.0.1. Generated 2024-06-18
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