Generated Narrative: StructureDefinition kps-specimen Name Flags Card. Type Description & Constraints<img src="[binary]" alt="doco" style="background-color: inherit"/> Specimen 0..* SpecimenUvIps Sample for analysis #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:priority S 0..1 CodeableConcept Specimen Priority URL: https://example.org/fhir/StructureDefinition/specimen-priority Binding: Specimen Priority ValueSet (preferred) #xD; extension:collectionContext S 0..1 CodeableConcept Collection Context URL: https://example.org/fhir/StructureDefinition/collection-context Binding: Specimen Collection ValueSet (preferred) #xD; status S 1..1 code available | unavailable | unsatisfactory | entered-in-error #xD; type S 1..1 CodeableConceptIPS Concept - reference to a terminology or just text Binding: Specimen Type ValueSet (required) #xD; subject S 1..1 Reference(Patient (IPS)) 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 #xD; receivedTime S 0..1 dateTime The time when specimen was received for processing #xD; collection S 0..1 BackboneElement Collection details #xD; collector S 0..1 Reference(Practitioner | PractitionerRole) Who collected the specimen #xD; collected[x] S 0..1 dateTime, Period Collection time #xD; processing S 0..* BackboneElement Processing and processing step details #xD; description S 0..1 string Textual description of procedure #xD; note S 0..* Annotation Comments #xD; <img src="[binary]" alt="doco" style="background-color: inherit"/> Documentation for this format
This profile defines constraints on the Specimen resource for use within the Kenya Patient Summary. It captures information about biological samples collected from a patient, supporting diagnostic procedures, continuity of care, and data exchange within the national Health Information Exchange (HIE).
If the resource is contained in another resource, it SHALL NOT contain nested Resources
not(parent::f:contained and f:contained)
If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource
contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))
If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))
If a resource is contained in another resource, it SHALL NOT have a security label
When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time.
A resource should have narrative for robust management
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.
All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
A set of rules under which this content was created
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.
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.
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).
Text summary of the resource, for human interpretation
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.
Must have either extensions or value[x], not both
exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
Urgency or priority with which the specimen was collected (e.g., STAT, routine).
exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])
Specifies the context of collection (e.g., surveillance, diagnostic, research).
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](http://hl7.org/fhir/R4/extensibility.html#modifierExtension).
Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
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.
.participation[typeCode=SBJ].act[classCode=ACSN, moodCode=EVN].id
available | unavailable | unsatisfactory | entered-in-error
This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid.
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
Codes providing the status/availability of a specimen.
Concept - reference to a terminology or just text
A concept that may be defined by a formal reference to a terminology or ontology or may be provided by text.
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.
Additional conformance binding to a specimen type value set from the SNOMED CT IPS free set for use globally (in SNOMED member and non-member jurisdictions).
fhir:CodeableConcept rdfs:subClassOf dt:CD
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.
Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Extensions are always sliced by (at least) url
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.
Literal reference, Relative, internal or absolute URL
A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.
Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure "/[type]/[id]" then it should be assumed that the reference is to a FHIR RESTful server.
Type the reference refers to (e.g. "Patient")
The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent. The type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. "Patient" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources).
This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified.
Aa resource (or, for logical models, the URI of the logical model).
Logical reference, when literal reference is not known
An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.
When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any).
Plain text narrative that identifies the resource in addition to the resource reference.
This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.
The time when specimen was received for processing
Time when specimen was received for processing or testing.
.participation[typeCode=SBJ].act[code=SPCREC, moodCode=EVN].effectiveTime
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.
.scoper (if parent) .player.scopesRole[classCode=SPEC].player (if child)
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.
Details concerning the specimen collection.
.participation[typeCode=SBJ].act[classCode=SPECCOLLECT, moodCode=EVN]
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).
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.
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.
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 'pre-coordinated 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).
Many diagnostic tests require fasting to facilitate accurate interpretation.
Codes describing the fasting status of the patient.
Details concerning processing and processing steps for the specimen.
.participation[typeCode=SBJ].act[code=SPCTRT, moodCode=EVN]
Indicates the treatment step applied to the specimen
A coded value specifying the procedure used to process the specimen.
Type indicating the technique used to process the specimen.
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.
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.
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.
Kind of container directly associated with specimen
The type of container associated with the specimen (e.g. slide, aliquot, etc.).
The capacity (volume or other measure) the container may contain.
one of: SAC 16, SAC17 and SAC 20, or SAC 21 and SAC 20
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.
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.
The specimen condition can be used to assess its quality or appropriateness for a specific test.
Codes describing the state of the specimen.
To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen).
.inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code="annotation"].value