Nexus EMR profile for Specimen -- the physical sample a lab result was produced from. Currently a pass-through type: the platform resolves ServiceRequest.specimen references and traverses into Specimen from DiagnosticReport, but reads none of its own fields. First pass; the heritage-EMR reconciliation is unresolved.
Elements / Details
Every element this profile touches, with its full definition. Element names in the tables link here.
A physical sample collected from a patient for examination.
In this platform, chiefly a pass-through and correlation resource: it links a result to the
sample and to the performing lab's accession. See the profile notes on the heritage-EMR
situation before building anything that depends on it being present.
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.
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.
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.
The version specific identifier, as it appears in the version portion of the URL. This value changes when the resource is created, updated, or deleted.
Comments
The server assigns this value, and ignores what the client specifies, except in the case that the server is imposing version integrity on updates/deletes.
When the resource last changed - e.g. when the version changed.
Comments
This value is always populated except when the resource is first being created. The server / resource manager sets this value; what a client provides is irrelevant. This is equivalent to the HTTP Last-Modified and SHOULD have the same value on a read interaction.
Identifies EMR instance & pipeline version the resource came from
Definition
A URI that identifies the EMR pipeline and version from which this resource originated. This tells you which EMR instance (recommend using the instance identifier), and the version of the pipeline code/transformations.
Comments
In the provenance resource, this corresponds to Provenance.entity.what[x]. The exact use of the source (and the implied Provenance.entity.role) is left to implementer discretion. Only one nominated source is allowed; for additional provenance details, a full Provenance resource should be used.
This element can be used to indicate where the current master source of a resource that has a canonical URL if the resource is no longer hosted at the canonical URL.
It is up to the server and/or other infrastructure of policy to determine whether/how these claims are verified and/or updated over time. The list of profile URLs is a set.
Security labels applied to this resource. These tags connect specific resources to the overall security policy and infrastructure.
Comments
The security labels can be updated without changing the stated version of the resource. The list of security labels is a set. Uniqueness is based the system/code, and version and display are ignored.
Tags applied to this resource. Tags are intended to be used to identify and relate resources to process and workflow, and applications are not required to consider the tags when interpreting the meaning of a resource.
Comments
The tags can be updated without changing the stated version of the resource. The list of tags is a set. Uniqueness is based the system/code, and version and display are ignored.
A set of rules under which this content was created
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.
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.
Cardinality
0..1
Type
uri
Modifier
yes — This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation
The base language in which the resource is written.
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).
A human-readable narrative summary of the NexusEmrCoreSpecimen resource for human interpretation.
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.
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.
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.
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.
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.
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).
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.
Cardinality
0..*
Type
Extension
Modifier
yes — Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
Identifiers for the specimen assigned by the collecting or receiving system.
A business identifier is recommended but not required (identifier is 0..*).
Distinct from accessionIdentifier below: this element is the specimen's own id in whatever system minted it; the accession is specifically the performing lab's.
⚠ HERITAGE EMR SITUATION -- UNRESOLVED. Heritage EMRs generally do NOT carry a first-class specimen record. A lab result arrives as an HL7 v2 message (or a rendered report) in which the specimen is implicit in the OBR segment, and no stable specimen identifier is minted at all. So for source-EMR-derived data this element is frequently absent, and where an ingest pipeline does populate it the value is typically synthesized rather than a real source key -- meaning it is NOT stable across re-ingests. Do not build correlation on it for heritage-sourced specimens; use accessionIdentifier, which the source message does carry. Whether ingest should mint synthetic specimen identifiers at all, and if so how to make them stable, is an open decision.
If no recognized system exists, implementers MAY invent a URI for the system.
Comments
A source system's own identifier SHOULD be carried alongside this one, flagged use = secondary. See Carrying the raw code.
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.
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.
A coded type for the identifier that can be used to determine which identifier to use for a specific purpose.
Requirements
Allows users to make use of identifiers when the identifier system is not known.
Comments
This element deals only with general categories of identifiers. It SHOULD not be used for codes that correspond 1..1 with the Identifier.system. Some identifiers may fall into multiple categories due to common usage. Where the system is known, a type is unnecessary because the type is always part of the system definition. However systems often need to handle identifiers where the system is not known. There is not a 1:1 relationship between type and system, since many different systems have the same type.
Establishes the namespace for the value - that is, a URL that describes a set values that are unique.
Requirements
There are many sets of identifiers. To perform matching of two identifiers, we need to know what set we're dealing with. The system identifies a particular set of unique identifiers.
The portion of the identifier typically relevant to the user and which is unique within the context of the system.
Comments
If the value is a full URI, then the system SHALL be urn:ietf:rfc:3986. The value's primary purpose is computational mapping. As a result, it may be normalized for comparison purposes (e.g. removing non-significant whitespace, dashes, etc.) A value formatted for human display can be conveyed using the Rendered Value extension. Identifier.value is to be treated as case sensitive unless knowledge of the Identifier.system allows the processer to be confident that non-case-sensitive processing is safe.
The Identifier.assigner may omit the .reference element and only contain a .display element reflecting the name or other textual information about the assigning organization.
The identifier assigned by the laboratory that processed the specimen.
This is the value that correlates a result back to the physical sample at the lab, and that reveals
when several results derive from a single draw. It is also what a human reads off a requisition when
phoning the lab, which makes it the identifier most often needed and most often missing.
⚠ HERITAGE EMR SITUATION -- UNRESOLVED. This is the one specimen field heritage EMRs reliably DO
carry, because it rides in the inbound HL7 v2 lab message. But it arrives without a governed system
URI: the accession is scoped to the performing lab and is not unique across labs, so two labs can
legitimately issue the same accession string. The IG does not yet define how to namespace it per
performing lab, so accessionIdentifier.system is currently unconstrained and inbound values may
collide. Treat an accession as unique only WITHIN a known performing organization until this is
resolved.
Comments
Do not merge with identifier -- an accession is lab-scoped and is not a substitute for a specimen identifier. See the definition for the unresolved cross-lab namespacing gap.
available | unavailable | unsatisfactory | entered-in-error
Definition
The availability of the specimen.
Comments
unsatisfactory is clinically meaningful -- a rejected sample means the test was NOT performed, and a consumer treating the linked result as pending rather than failed will wait forever. 0..1 in R4, so absence must be tolerated and must NOT be read as available. Heritage-EMR-derived specimens usually carry no status at all.
Cardinality
0..1
Type
code
Must Support
yes
Modifier
yes — This element is labelled as a modifier because it is a status element that contains status entered-in-error which means that the resource should not be treated as valid
⚠ FIRST PASS -- no binding. The SNOMED specimen hierarchy is large and no agreed subset exists for this EMR. Readers MUST tolerate text-only. Heritage-EMR data typically supplies at most a free-text specimen-source string from the HL7 v2 OBR segment, so text-only is the expected shape, not the exception. Where this code was mapped from a source system's own vocabulary, carry the raw coding alongside the mapped one, flagged userSelected = true. See Carrying the raw code.
The patient the specimen was collected from.
0..1 in R4 (a specimen can be environmental or device-derived) and left optional here. Anything
appearing in a patient chart MUST carry it.
⚠ HERITAGE EMR SITUATION -- UNRESOLVED. Where a Specimen is synthesized during lab ingest, the
patient link is inferred from the enclosing DiagnosticReport rather than carried by the source
message. That inference is only as good as the report's own patient matching, so a mis-matched
report propagates its error into the specimen silently. Whether ingest-synthesized specimens should
assert subject at all -- versus leaving it absent and letting consumers reach the patient through
DiagnosticReport.subject -- is unresolved.
Reference to the parent (source) specimen which is used when the specimen was either derived from or a component of another 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.
Details concerning a service request that required a specimen to be collected.
Comments
The inverse of ServiceRequest.specimen, which the eReferral reference resolver rewrites when relaying a message bundle. Per the logical-reference model these MAY be identifier-only.
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.
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.
Extensions that cannot be ignored even if unrecognized
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).
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.
Cardinality
0..*
Type
Extension
Modifier
yes — Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Time when specimen was collected from subject - the physiologically relevant time.
Comments
THE effective date for this profile, preferred over receivedTime. A choice of dateTime or Period in R4 -- handle both. Heritage-EMR lab messages often carry only the received/report time, in which case this is absent and the effective date falls through to receivedTime.
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.
Whether or how long patient abstained from food and/or drink
Definition
Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection.
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 such asObservation.component code` = LOINC 49541-6 (Fasting status - Reported).
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.
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.
Extensions that cannot be ignored even if unrecognized
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).
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.
Cardinality
0..*
Type
Extension
Modifier
yes — Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
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.
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.
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.
Extensions that cannot be ignored even if unrecognized
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).
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.
Cardinality
0..*
Type
Extension
Modifier
yes — Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
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.
A mode or state of being that describes the nature of the specimen.
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.