Path | Short | Definition | Comments |
---|---|---|---|
Sample for analysis | A sample to be used for analysis. | ||
identifier | External Identifier | Id for specimen. | |
accessionIdentifier | Identifier assigned by the lab | 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. | |
status | available | unavailable | unsatisfactory | entered-in-error | The availability of the specimen. | This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid. |
type | Kind of material that forms the specimen | 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. |
subject | 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 | 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. | |
receivedTime | The time when specimen was received for processing | Time when specimen was received for processing or testing. | |
parent | Specimen from which this specimen originated | 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. |
request | Why the specimen was collected | 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. |
collection | Collection details | Details concerning the specimen collection. | |
collection.id | Unique id for inter-element referencing | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. | |
collection.extension | Additional content defined by implementations | 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. |
collection.modifierExtension | Extensions that cannot be ignored even if unrecognized | 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. |
collection.collector | Who collected the specimen | Person who collected the specimen. | |
collection.collected[x] | Collection time | Time when specimen was collected from subject - the physiologically relevant time. | |
collection.duration | How long it took to collect specimen | The span of time over which the collection of a specimen occurred. | |
collection.quantity | The quantity of specimen collected | The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology sample. | |
collection.method | Technique used to perform collection | A coded value specifying the technique that is used to perform the procedure. | |
collection.bodySite | Anatomical collection site | 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](extension-bodysite.html). |
collection.fastingStatus[x] | Whether or how long patient abstained from food and/or drink | 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 'precoordinated code' such as LOINC 2005-7 (Calcium [Moles/time] in 2 hour Urine --12 hours fasting), or using a component observation ` such as `Observation.component code` = LOINC 49541-6 (Fasting status - Reported). |
processing | Processing and processing step details | Details concerning processing and processing steps for the specimen. | |
processing.id | Unique id for inter-element referencing | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. | |
processing.extension | Additional content defined by implementations | 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. |
processing.modifierExtension | Extensions that cannot be ignored even if unrecognized | 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. |
processing.description | Textual description of procedure | Textual description of procedure. | |
processing.procedure | Indicates the treatment step applied to the specimen | A coded value specifying the procedure used to process the specimen. | |
processing.additive | Material used in the processing step | Material used in the processing step. | |
processing.time[x] | Date and time of specimen processing | 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. | |
container | Direct container of specimen (tube/slide, etc.) | The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed here. | |
container.id | Unique id for inter-element referencing | Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. | |
container.extension | Additional content defined by implementations | 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. |
container.modifierExtension | Extensions that cannot be ignored even if unrecognized | 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. |
container.identifier | Id for the container | 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. | |
container.description | Textual description of the container | Textual description of the container. | |
container.type | Kind of container directly associated with specimen | The type of container associated with the specimen (e.g. slide, aliquot, etc.). | |
container.capacity | Container volume or size | The capacity (volume or other measure) the container may contain. | |
container.specimenQuantity | Quantity of specimen within container | The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type. | |
container.additive[x] | Additive associated with container | Introduced substance to preserve, maintain or enhance the specimen. Examples: Formalin, Citrate, EDTA. | |
condition | State of the specimen | 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 it's quality or it's appropriateness for a specific test. |
note | Comments | To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen). |
Any material sample:
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, biobanking, etc. Comments from reviewers on the appropriate scope for this resource, and the need for tracking related specimen management attributes, are welcomed.
accession | The accession number associated with the specimen | Specimen.accessionIdentifier |
bodysite | The code for the body site from where the specimen originated | Specimen.collection.bodySite |
collected | The date the specimen was collected | Specimen.collection.collected |
collector | Who collected the specimen | Specimen.collection.collector |
container | The kind of specimen container | Specimen.container.type |
container-id | The unique identifier associated with the specimen container | Specimen.container.identifier |
identifier | The unique identifier associated with the specimen | Specimen.identifier |
parent | The parent of the specimen | Specimen.parent |
patient | The patient the specimen comes from | Specimen.subject.where(resolve() is Patient) |
status | available | unavailable | unsatisfactory | entered-in-error | Specimen.status |
subject | The subject of the specimen | Specimen.subject |
type | The specimen type | Specimen.type |