Specimen
Defines the ID Core constraints and extensions on the Specimen resource for the minimal set of data to query and retrieve specimen information.
Usage
The purpose of this resources is to provide detailed information about any material sample taken from a biological entity (living or dead) or taken from a phyisical object (or the environment).
Some specimens are biological and can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products.
The specimen resource covers substances used for diagnostic and environmental testing. The focus of the specimen resource is the process for gathering, maintaining and processing the specimen as well as where the specimen originated. This is distinct from the use of Substance which is only used when these other aspects are not relevant.
URL
Type | URL |
---|---|
Canonical | https://fhir.kemkes.go.id/r4/StructureDefinition/Specimen |
Structure
Snapshot
Specimen | I | DomainResource | |
id | Σ | 0..1 | string |
meta | Σ | 0..1 | Meta |
implicitRules | Σ ?! | 0..1 | uri |
language | 0..1 | codeBinding | |
text | 0..1 | Narrative | |
contained | 0..* | Resource | |
extension | 1.. | ||
transportedTime | I | 1..1 | Extension(dateTime) |
identifier | Σ | 0..* | Identifier |
accessionIdentifier | Σ | 0..1 | Identifier |
status | Σ ?! | 1..1 | codeBinding |
type | Σ | 1..1 | CodeableConcept |
subject | Σ I | 1..1 | Reference(Patient | https://fhir.kemkes.go.id/r4/StructureDefinition/Group | | https://fhir.kemkes.go.id/r4/StructureDefinition/Substance | Location) |
receivedTime | Σ | 0..1 | dateTime |
parent | I | 0..* | Reference(Specimen) |
request | I | 0..* | Reference(ServiceRequest) |
collection | 0..1 | BackboneElement | |
id | 0..1 | string | |
extension | I | 0..* | Extension |
collectorOrganization | I | 0..* | Extension |
modifierExtension | Σ ?! I | 0..* | Extension |
collector | Σ I | 0..1 | Reference(Practitioner | PractitionerRole) |
collected[x] | Σ | 0..1 | |
collectedDateTime | dateTime | ||
collectedPeriod | Period | ||
duration | Σ I | 0..1 | Duration |
quantity | I | 0..1 | SimpleQuantity |
method | 0..1 | CodeableConcept | |
bodySite | 0..1 | CodeableConcept | |
fastingStatus[x] | Σ | 0..1 | Binding |
fastingStatusCodeableConcept | CodeableConcept | ||
fastingStatusDuration | Duration | ||
processing | 0..* | BackboneElement | |
id | 0..1 | string | |
extension | I | 0..* | Extension |
modifierExtension | Σ ?! I | 0..* | Extension |
description | 0..1 | string | |
procedure | 0..1 | CodeableConcept | |
additive | I | 0..* | Reference(https://fhir.kemkes.go.id/r4/StructureDefinition/Substance) |
time[x] | 0..1 | ||
timeDateTime | dateTime | ||
timePeriod | Period | ||
container | 0..* | BackboneElement | |
id | 0..1 | string | |
extension | I | 0..* | Extension |
modifierExtension | Σ ?! I | 0..* | Extension |
identifier | Σ | 0..* | Identifier |
description | 0..1 | string | |
type | 0..1 | CodeableConcept | |
capacity | I | 0..1 | SimpleQuantity |
specimenQuantity | I | 0..1 | SimpleQuantity |
additive[x] | 0..1 | ||
additiveCodeableConcept | CodeableConcept | ||
additiveReference | Reference(https://fhir.kemkes.go.id/r4/StructureDefinition/Substance) | ||
condition | Σ | 0..* | CodeableConceptBinding |
note | 0..* | Annotation |
Examples
Dictionary
Specimen | |
Definition | A sample to be used for analysis. |
Cardinality | 0...* |
Invariants |
|
Mappings |
|
Specimen.id | |
Definition | The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. |
Cardinality | 0...1 |
Type | string |
Summary | True |
Comments | The only time that a resource does not have an id is when it is being submitted to the server using a create operation. |
Specimen.meta | |
Definition | The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource. |
Cardinality | 0...1 |
Type | Meta |
Summary | True |
Invariants |
|
Mappings |
|
Specimen.implicitRules | |
Definition | A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc. |
Cardinality | 0...1 |
Type | uri |
Modifier | True |
Summary | True |
Comments | Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc. |
Invariants |
|
Mappings |
|
Specimen.language | |
Definition | The base language in which the resource is written. |
Cardinality | 0...1 |
Type | code |
Binding | A human language. |
Comments | Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute). |
Invariants |
|
Mappings |
|
Specimen.text | |
Definition | A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety. |
Cardinality | 0...1 |
Type | Narrative |
Alias | narrative, html, xhtml, display |
Comments | Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later. |
Invariants |
|
Mappings |
|
Specimen.contained | |
Definition | These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope. |
Cardinality | 0...* |
Type | Resource |
Alias | inline resources, anonymous resources, contained resources |
Comments | This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels. |
Mappings |
|
Specimen.extension | |
Cardinality | 1 |
Slicing | Unordered, Open, by url(Value) |
Specimen.extension:transportedTime | |
Definition | When the sample transported |
Cardinality | 1...1 |
Type | Extension(dateTime) |
Invariants |
|
Mappings |
|
Specimen.identifier | |
Definition | Id for specimen. |
Cardinality | 0...* |
Type | Identifier |
Summary | True |
Invariants |
|
Mappings |
|
Specimen.accessionIdentifier | |
Definition | The identifier assigned by the lab when accessioning specimen(s). This is not necessarily the same as the specimen identifier, depending on local lab procedures. |
Cardinality | 0...1 |
Type | Identifier |
Summary | True |
Invariants |
|
Mappings |
|
Specimen.status | |
Definition | The availability of the specimen. |
Cardinality | 1...1 |
Type | code |
Binding | Codes providing the status/availability of a specimen. |
Modifier | True |
Summary | True |
Comments | This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid. |
Invariants |
|
Mappings |
|
Specimen.type | |
Definition | The kind of material that forms the specimen. |
Cardinality | 1...1 |
Type | CodeableConcept |
Binding | The type of the specimen. |
Summary | True |
Comments | The type can change the way that a specimen is handled and drives what kind of analyses can properly be performed on the specimen. It is frequently used in diagnostic work flow decision making systems. |
Invariants |
|
Mappings |
|
Specimen.subject | |
Definition | Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device. |
Cardinality | 1...1 |
Type | Reference(Patient | https://fhir.kemkes.go.id/r4/StructureDefinition/Group | | https://fhir.kemkes.go.id/r4/StructureDefinition/Substance | Location) |
Summary | True |
Requirements | Must know the subject context. |
Comments | References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. |
Invariants |
|
Mappings |
|
Specimen.receivedTime | |
Definition | Time when specimen was received for processing or testing. |
Cardinality | 0...1 |
Type | dateTime |
Summary | True |
Invariants |
|
Mappings |
|
Specimen.parent | |
Definition | Reference to the parent (source) specimen which is used when the specimen was either derived from or a component of another specimen. |
Cardinality | 0...* |
Type | Reference(Specimen) |
Comments | The parent specimen could be the source from which the current specimen is derived by some processing step (e.g. an aliquot or isolate or extracted nucleic acids from clinical samples) or one of many specimens that were combined to create a pooled sample. |
Invariants |
|
Mappings |
|
Specimen.request | |
Definition | Details concerning a service request that required a specimen to be collected. |
Cardinality | 0...* |
Type | Reference(ServiceRequest) |
Comments | The request may be explicit or implied such with a ServiceRequest that requires a blood draw. |
Invariants |
|
Mappings |
|
Specimen.collection | |
Definition | Details concerning the specimen collection. |
Cardinality | 0...1 |
Type | BackboneElement |
Invariants |
|
Mappings |
|
Specimen.collection.id | |
Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
Cardinality | 0...1 |
Type | string |
Mappings |
|
Specimen.collection.extension | |
Definition | May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. |
Cardinality | 0...* |
Type | Extension |
Alias | extensions, user content |
Comments | There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. |
Slicing | Unordered, Open, by url(Value) |
Invariants |
|
Mappings |
|
Specimen.collection.extension:collectorOrganization | |
Definition | May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. |
Cardinality | 0...* |
Type | Extension |
Alias | extensions, user content |
Comments | There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. |
Invariants |
|
Mappings |
|
Specimen.collection.modifierExtension | |
Definition | May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). |
Cardinality | 0...* |
Type | Extension |
Modifier | True |
Summary | True |
Alias | extensions, user content, modifiers |
Requirements | Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions. |
Comments | There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. |
Invariants |
|
Mappings |
|
Specimen.collection.collector | |
Definition | Person who collected the specimen. |
Cardinality | 0...1 |
Type | Reference(Practitioner | PractitionerRole) |
Summary | True |
Comments | References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. |
Invariants |
|
Mappings |
|
Specimen.collection.collected[x] | |
Definition | Time when specimen was collected from subject - the physiologically relevant time. |
Cardinality | 0...1 |
Type | dateTime |
Summary | True |
Invariants |
|
Mappings |
|
Specimen.collection.duration | |
Definition | The span of time over which the collection of a specimen occurred. |
Cardinality | 0...1 |
Type | Duration |
Summary | True |
Comments | The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator. |
Invariants |
|
Mappings |
|
Specimen.collection.quantity | |
Definition | The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology sample. |
Cardinality | 0...1 |
Type | SimpleQuantity |
Comments | The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator. |
Invariants |
|
Mappings |
|
Specimen.collection.method | |
Definition | A coded value specifying the technique that is used to perform the procedure. |
Cardinality | 0...1 |
Type | CodeableConcept |
Binding | The technique that is used to perform the procedure. |
Comments | Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. |
Invariants |
|
Mappings |
|
Specimen.collection.bodySite | |
Definition | Anatomical location from which the specimen was collected (if subject is a patient). This is the target site. This element is not used for environmental specimens. |
Cardinality | 0...1 |
Type | CodeableConcept |
Binding | Codes describing anatomical locations. May include laterality. |
Comments | If the use case requires BodySite to be handled as a separate resource instead of an inline coded element (e.g. to identify and track separately) then use the standard extension bodySite. |
Invariants |
|
Mappings |
|
Specimen.collection.fastingStatus[x] | |
Definition | Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection. |
Cardinality | 0...1 |
Type | CodeableConcept |
Binding | Codes describing the fasting status of the patient. |
Summary | True |
Requirements | Many diagnostic tests require fasting to facilitate accurate interpretation. |
Comments | Representing fasting status using this element is preferred to representing it with an observation using a 'pre-coordinated code' such as LOINC 2005-7 (Calcium [Moles/time] in 2 hour Urine --12 hours fasting), or using a component observation |
Invariants |
|
Mappings |
|
Specimen.processing | |
Definition | Details concerning processing and processing steps for the specimen. |
Cardinality | 0...* |
Type | BackboneElement |
Invariants |
|
Mappings |
|
Specimen.processing.id | |
Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
Cardinality | 0...1 |
Type | string |
Mappings |
|
Specimen.processing.extension | |
Definition | May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. |
Cardinality | 0...* |
Type | Extension |
Alias | extensions, user content |
Comments | There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. |
Slicing | Unordered, Open, by url(Value) |
Invariants |
|
Mappings |
|
Specimen.processing.modifierExtension | |
Definition | May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). |
Cardinality | 0...* |
Type | Extension |
Modifier | True |
Summary | True |
Alias | extensions, user content, modifiers |
Requirements | Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions. |
Comments | There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. |
Invariants |
|
Mappings |
|
Specimen.processing.description | |
Definition | Textual description of procedure. |
Cardinality | 0...1 |
Type | string |
Comments | Note that FHIR strings SHALL NOT exceed 1MB in size |
Invariants |
|
Mappings |
|
Specimen.processing.procedure | |
Definition | A coded value specifying the procedure used to process the specimen. |
Cardinality | 0...1 |
Type | CodeableConcept |
Binding | Type indicating the technique used to process the specimen. |
Comments | Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. |
Invariants |
|
Mappings |
|
Specimen.processing.additive | |
Definition | Material used in the processing step. |
Cardinality | 0...* |
Type | Reference(https://fhir.kemkes.go.id/r4/StructureDefinition/Substance) |
Comments | References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. |
Invariants |
|
Mappings |
|
Specimen.processing.time[x] | |
Definition | A record of the time or period when the specimen processing occurred. For example the time of sample fixation or the period of time the sample was in formalin. |
Cardinality | 0...1 |
Type | dateTime |
Invariants |
|
Mappings |
|
Specimen.container | |
Definition | The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed here. |
Cardinality | 0...* |
Type | BackboneElement |
Invariants |
|
Mappings |
|
Specimen.container.id | |
Definition | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
Cardinality | 0...1 |
Type | string |
Mappings |
|
Specimen.container.extension | |
Definition | May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. |
Cardinality | 0...* |
Type | Extension |
Alias | extensions, user content |
Comments | There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. |
Slicing | Unordered, Open, by url(Value) |
Invariants |
|
Mappings |
|
Specimen.container.modifierExtension | |
Definition | May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). |
Cardinality | 0...* |
Type | Extension |
Modifier | True |
Summary | True |
Alias | extensions, user content, modifiers |
Requirements | Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions. |
Comments | There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. |
Invariants |
|
Mappings |
|
Specimen.container.identifier | |
Definition | Id for container. There may be multiple; a manufacturer's bar code, lab assigned identifier, etc. The container ID may differ from the specimen id in some circumstances. |
Cardinality | 0...* |
Type | Identifier |
Summary | True |
Invariants |
|
Mappings |
|
Specimen.container.description | |
Definition | Textual description of the container. |
Cardinality | 0...1 |
Type | string |
Comments | Note that FHIR strings SHALL NOT exceed 1MB in size |
Invariants |
|
Mappings |
|
Specimen.container.type | |
Definition | The type of container associated with the specimen (e.g. slide, aliquot, etc.). |
Cardinality | 0...1 |
Type | CodeableConcept |
Binding | Type of specimen container. |
Comments | Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. |
Invariants |
|
Mappings |
|
Specimen.container.capacity | |
Definition | The capacity (volume or other measure) the container may contain. |
Cardinality | 0...1 |
Type | SimpleQuantity |
Comments | The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator. |
Invariants |
|
Mappings |
|
Specimen.container.specimenQuantity | |
Definition | The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type. |
Cardinality | 0...1 |
Type | SimpleQuantity |
Comments | The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator. |
Invariants |
|
Mappings |
|
Specimen.container.additive[x] | |
Definition | Introduced substance to preserve, maintain or enhance the specimen. Examples: Formalin, Citrate, EDTA. |
Cardinality | 0...1 |
Type | CodeableConcept |
Binding | Substance added to specimen container. |
Invariants |
|
Mappings |
|
Specimen.condition | |
Definition | A mode or state of being that describes the nature of the specimen. |
Cardinality | 0...* |
Type | CodeableConcept |
Binding | Codes describing the state of the specimen. |
Summary | True |
Requirements | The specimen condition can be used to assess its quality or appropriateness for a specific test. |
Comments | Specimen condition is an observation made about the specimen. It's a point-in-time assessment. It can be used to assess its quality or appropriateness for a specific test. |
Invariants |
|
Mappings |
|
Specimen.note | |
Definition | To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen). |
Cardinality | 0...* |
Type | Annotation |
Comments | For systems that do not have structured annotations, they can simply communicate a single annotation with no author or time. This element may need to be included in narrative because of the potential for modifying information. Annotations SHOULD NOT be used to communicate "modifying" information that could be computable. (This is a SHOULD because enforcing user behavior is nearly impossible). |
Invariants |
|
Mappings |
|