Specimen | Medplum
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A sample to be used for analysis.
- Schema
- Usage
- Background and Context
- Referenced By
Elements
| Name | Required | Type | Description |
|---|---|---|---|
| identifier | Identifier[] | External Identifier Details Id for specimen. |
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| accessionIdentifier | Identifier | Identifier assigned by the lab Details 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. |
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| status | code | available | |
| type | CodeableConcept | Kind of material that forms the specimen Details The kind of material that forms the specimen. 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. |
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| subject | Reference< Patient |
Group |
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| receivedTime | dateTime | The time when specimen was received for processing Details Time when specimen was received for processing or testing. |
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| parent | Reference< Specimen >[] | Specimen from which this specimen originated Details Reference to the parent (source) specimen which is used when the specimen was either derived from or a component of another specimen. 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. |
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| request | Reference< ServiceRequest >[] | Why the specimen was collected Details Details concerning a service request that required a specimen to be collected. The request may be explicit or implied such with a ServiceRequest that requires a blood draw. |
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| collection | SpecimenCollection | Collection details Details Details concerning the specimen collection. |
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| id | string | Unique id for inter-element referencing Details Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
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| extension | Extension[] | Additional content defined by implementations Details 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. 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. |
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| modifierExtension | Extension[] | Extensions that cannot be ignored even if unrecognized Details 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). 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. |
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| collector | Reference< Practitioner | PractitionerRole > | |
| collected[x] | dateTime, Period | Collection time Details Time when specimen was collected from subject - the physiologically relevant time. |
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| duration | Duration | How long it took to collect specimen Details The span of time over which the collection of a specimen occurred. |
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| quantity | Quantity | The quantity of specimen collected Details The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology sample. |
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| method | CodeableConcept | Technique used to perform collection Details A coded value specifying the technique that is used to perform the procedure. |
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| bodySite | CodeableConcept | Anatomical collection site Details 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. 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. |
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| fastingStatus[x] | CodeableConcept, Duration | Whether or how long patient abstained from food and/or drink Details Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection. 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 such asObservation.component code` = LOINC 49541-6 (Fasting status - Reported). |
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| processing | SpecimenProcessing[] | Processing and processing step details Details Details concerning processing and processing steps for the specimen. |
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| id | string | Unique id for inter-element referencing Details Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
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| extension | Extension[] | Additional content defined by implementations Details 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. 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. |
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| modifierExtension | Extension[] | Extensions that cannot be ignored even if unrecognized Details 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). 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. |
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| description | string | Textual description of procedure Details Textual description of procedure. |
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| procedure | CodeableConcept | Indicates the treatment step applied to the specimen Details A coded value specifying the procedure used to process the specimen. |
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| additive | Reference< Substance >[] | Material used in the processing step Details Material used in the processing step. |
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| time[x] | dateTime, Period | Date and time of specimen processing Details 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. |
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| container | SpecimenContainer[] | Direct container of specimen (tube/slide, etc.) Details The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed here. |
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| id | string | Unique id for inter-element referencing Details Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. |
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| extension | Extension[] | Additional content defined by implementations Details 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. 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. |
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| modifierExtension | Extension[] | Extensions that cannot be ignored even if unrecognized Details 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). 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. |
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| identifier | Identifier[] | Id for the container Details 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. |
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| description | string | Textual description of the container Details Textual description of the container. |
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| type | CodeableConcept | Kind of container directly associated with specimen Details The type of container associated with the specimen (e.g. slide, aliquot, etc.). |
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| capacity | Quantity | Container volume or size Details The capacity (volume or other measure) the container may contain. |
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| specimenQuantity | Quantity | Quantity of specimen within container Details The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type. |
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| additive[x] | CodeableConcept, Reference< Substance >[] | Additive associated with container Details Introduced substance to preserve, maintain or enhance the specimen. Examples: Formalin, Citrate, EDTA. |
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| condition | CodeableConcept[] | State of the specimen Details A mode or state of being that describes the nature of the specimen. 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. |
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| note | Annotation[] | Comments Details To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen). |
Search Parameters
| Name | Type | Description | Expression |
|---|---|---|---|
| accession | token | The accession number associated with the specimen | Specimen.accessionIdentifier |
| bodysite | token | The code for the body site from where the specimen originated | Specimen.collection.bodySite |
| collected | date | The date the specimen was collected | Specimen.collection.collected |
| collector | reference | Who collected the specimen | Specimen.collection.collector |
| container | token | The kind of specimen container | Specimen.container.type |
| container-id | token | The unique identifier associated with the specimen container | Specimen.container.identifier |
| identifier | token | The unique identifier associated with the specimen | Specimen.identifier |
| parent | reference | The parent of the specimen | Specimen.parent |
| patient | reference | The patient the specimen comes from | Specimen.subject.where((resolve() is Patient)) |
| status | token | available | unavailable |
| subject | reference | The subject of the specimen | Specimen.subject |
| type | token | The specimen type | Specimen.type |
Inherited Elements
| Name | Required | Type | Description |
|---|---|---|---|
| id | string | Logical id of this artifact Details The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. The only time that a resource does not have an id is when it is being submitted to the server using a create operation. |
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| meta | Meta | Metadata about the resource Details 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. |
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| implicitRules | uri | A set of rules under which this content was created Details 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. 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. |
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| language | code | Language of the resource content Details The base language in which the resource is written. 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). |
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| text | Narrative | Text summary of the resource, for human interpretation Details 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. 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). |
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| contained | Resource[] | Contained, inline Resources Details 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. 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. |
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| extension | Extension[] | Additional content defined by implementations Details May be used to represent additional information that is not part of the basic definition of the resource. 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. 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. |
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| modifierExtension | Extension[] | Extensions that cannot be ignored Details May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it 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 is allowed to 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). 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. |
Any material sample:
- taken from a biological entity, living or dead
- taken from a physical 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 (source: NCI Thesaurus, modified).
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.
The current definition of the specimen resource contains only basic information about specimen containers. It does not address the recursive nature of containers or the tracking of the location of a container within its parent container (for instance: a tube in a tray in a rack in a freezer). The frequency with which these elements are tracked may depend on the context of use; general lab, bio-banking, etc. Comments from reviewers on the appropriate scope for this resource, and the need for tracking related specimen management attributes, are welcomed.