Laboratory specimen

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.

An Extension

Specimen focus, Extension to represent the entity from which the specimen is collected when it is not the subject of record.

For an animal specimen source the AnimalSpecimenEuLab profile is expected to be used.

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.

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.

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.

Codes providing the status/availability of a specimen.

The kind of material that forms the specimen.

If the specimen.type conveys information about the site the specimen has been collected from, then, if the bodySite if present it shall be coherent with the type. For a non-identifiable animal specimen source (e.g. 710069003 | Tick specimen (specimen) |), Specimen.type with the appropriate code shall be used.

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.

Must know the subject context.

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.

Details concerning a service request that required a specimen to be collected.

If the specimen information are known when the order is created then the ServiceRequest.specimen should be used. If the ServiceRequest can be updated when the specimen is collected then the ServiceRequest.specimen or the Specimen.request could be used. Otherwise the relationship is recorded in the Specimen.request element

Laboratory specimen

For an animal specimen source the AnimalSpecimenEuLab profile is expected to be used.

If the specimen.type conveys information about the site the specimen has been collected from, then, if the bodySite if present it shall be coherent with the type. For a non-identifiable animal specimen source (e.g. 710069003 | Tick specimen (specimen) |), Specimen.type with the appropriate code shall be used.

If the specimen information are known when the order is created then the ServiceRequest.specimen should be used. If the ServiceRequest can be updated when the specimen is collected then the ServiceRequest.specimen or the Specimen.request could be used. Otherwise the relationship is recorded in the Specimen.request element

If the specimen.type conveys information about the site the specimen has been collected from, then, if the bodySite is present, it shall be coherent with the type

Laboratory specimen

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.

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.

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.

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).

A human language.

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). 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.

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.

An Extension

Specimen focus, Extension to represent the entity from which the specimen is collected when it is not the subject of record.

For an animal specimen source the AnimalSpecimenEuLab profile is expected to be used.

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.

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.

Id for specimen.

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.

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.

Codes providing the status/availability of a specimen.

The kind of material that forms the specimen.

If the specimen.type conveys information about the site the specimen has been collected from, then, if the bodySite if present it shall be coherent with the type. For a non-identifiable animal specimen source (e.g. 710069003 | Tick specimen (specimen) |), Specimen.type with the appropriate code shall be used.

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.

Must know the subject context.

Time when specimen was received for processing or testing.

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.

Details concerning a service request that required a specimen to be collected.

If the specimen information are known when the order is created then the ServiceRequest.specimen should be used. If the ServiceRequest can be updated when the specimen is collected then the ServiceRequest.specimen or the Specimen.request could be used. Otherwise the relationship is recorded in the Specimen.request element

Details concerning the specimen collection.

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

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.

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.

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.

Person who collected the specimen.

Time when specimen was collected from subject - the physiologically relevant time.

The span of time over which the collection of a specimen occurred.

The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology sample.

A coded value specifying the technique that is used to perform the procedure.

The technique that is used to perform the procedure.

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 specimen.type conveys information about the site the specimen has been collected from, then, if the bodySite is present, it shall be coherent with the type

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

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.

R5: Specimen.collection.bodySite additional types (CodeableReference(http://hl7.org/fhir/StructureDefinition/BodyStructure)) additional types from child elements (reference)

Element Specimen.collection.bodySite is mapped to FHIR R4 element Specimen.collection.bodySite as SourceIsBroaderThanTarget. The mappings for Specimen.collection.bodySite do not cover the following types: CodeableReference. The mappings for Specimen.collection.bodySite do not cover the following types based on type expansion: reference. Reasons for using BodyStructure reference include: 1.) Need to identify a specific site instance (e.g. a specific mole), 2.) a single pre-coordinated coded concept for the body site does not exist, 3.) a desire to represent bodySite using multiple attributes (e.g. modifiers).

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

An Extension

Source of the definition for the extension code - a logical name or a URL.

The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.

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.

Reasons for using BodyStructure reference include: 1.) Need to identify a specific site instance (e.g. a specific mole), 2.) a single pre-coordinated coded concept for the body site does not exist, 3.) a desire to represent bodySite using multiple attributes (e.g. modifiers).

A reference to a code defined by a terminology system.

Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.

Allows for alternative encodings within a code system, and translations to other code systems.

A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.

Very often the text is the same as a displayName of one of the codings.

The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source.

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).

Codes describing the fasting status of the patient.

Many diagnostic tests require fasting to facilitate accurate interpretation.

Details concerning processing and processing steps for the specimen.

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

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.

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.

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.

Textual description of procedure.

A coded value specifying the procedure used to process the specimen.

Type indicating the technique used to process the specimen.

Material used in the processing step.

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.

The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed here.

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

An Extension

R5: Specimen.container.device (new:Reference(Device))

Element Specimen.container.device has a context of Specimen.container based on following the parent source element upwards and mapping to Specimen. Element Specimen.container.device has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element).

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

An Extension

Source of the definition for the extension code - a logical name or a URL.

The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.

The device resource for the the container holding the specimen. If the container is in a holder then the referenced device will point to a parent device.

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.

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.

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.

Textual description of the container.

The type of container associated with the specimen (e.g. slide, aliquot, etc.).

The capacity (volume or other measure) the container may contain.

The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type.

Introduced substance to preserve, maintain or enhance the specimen. Examples: Formalin, Citrate, EDTA.

Substance added to specimen container.

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.

Codes describing the state of the specimen.

The specimen condition can be used to assess its quality or appropriateness for a specific test.

To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen).