Botswana FHIR Implementation Guide
1.0.0 - STU1 Botswana flag

Botswana FHIR Implementation Guide, published by Jembi Health Systems. This guide is not an authorized publication; it is the continuous build for version 1.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/jembi/botswana-hie-fhir-ig/ and changes regularly. See the Directory of published versions

Resource Profile: LabOrderSpecimen - Detailed Descriptions

Active as of 2025-03-17

Definitions for the lab-order-specimen resource profile.

Guidance on how to interpret the contents of this table can be found here

0. Specimen
Definition

A sample to be used for analysis.

ShortSample for analysis
Control0..*
Is Modifierfalse
Summaryfalse
Invariantsdom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources (contained.contained.empty())
dom-3: 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())
dom-4: 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())
dom-5: If a resource is contained in another resource, it SHALL NOT have a security label (contained.meta.security.empty())
dom-6: A resource should have narrative for robust management (text.`div`.exists())
2. Specimen.implicitRules
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.

ShortA set of rules under which this content was created
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.

Control0..1
Typeuri
Is Modifiertrue because 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
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
Summarytrue
Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
4. Specimen.modifierExtension
Definition

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).

ShortExtensions that cannot be ignored
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.

Control0..*
TypeExtension
Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
Summaryfalse
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.

Alternate Namesextensions, user content
Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
6. Specimen.identifier
Definition

reasons why this should be supported


Id for specimen.

ShortExternal Identifier
NoteThis is a business identifier, not a resource identifier (see discussion)
Control10..*
TypeIdentifier
Is Modifierfalse
Summarytrue
Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
SlicingThis element introduces a set of slices on Specimen.identifier. The slices areUnordered and Open, and can be differentiated using the following discriminators:
  • value @ system
  • 8. Specimen.identifier:USID
    Slice NameUSID
    Definition

    Id for specimen.

    ShortExternal Identifier
    NoteThis is a business identifier, not a resource identifier (see discussion)
    Control10..1*
    TypeIdentifier
    Is Modifierfalse
    Summarytrue
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    10. Specimen.identifier:USID.use
    Definition

    The purpose of this identifier.

    Shortusual | official | temp | secondary | old (If known)
    Comments

    Applications can assume that an identifier is permanent unless it explicitly says that it is temporary.

    Control0..1
    BindingThe codes SHALL be taken from IdentifierUsehttp://hl7.org/fhir/ValueSet/identifier-use|4.0.1
    (required to http://hl7.org/fhir/ValueSet/identifier-use|4.0.1)

    Identifies the purpose for this identifier, if known .

    Typecode
    Is Modifiertrue because This is labeled as "Is Modifier" because applications should not mistake a temporary id for a permanent one.
    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
    Summarytrue
    Requirements

    Allows the appropriate identifier for a particular context of use to be selected from among a set of identifiers.

    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    12. Specimen.identifier:USID.system
    Definition

    Establishes the namespace for the value - that is, a URL that describes a set values that are unique.

    ShortThe namespace for the identifier value
    Comments

    Identifier.system is always case sensitive.

    Control10..1
    Typeuri
    Is Modifierfalse
    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
    Summarytrue
    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.

    Pattern Valuehttp://moh.bw.org/identifier/specimen-id
    Example<br/><b>General</b>:http://www.acme.com/identifiers/patient
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    14. Specimen.identifier:USID.value
    Definition

    The portion of the identifier typically relevant to the user and which is unique within the context of the system.

    ShortThe value that is unique
    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.

    Control10..1
    Typestring
    Is Modifierfalse
    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
    Summarytrue
    Example<br/><b>General</b>:123456
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    16. Specimen.status
    Definition

    The availability of the specimen.

    Shortavailable | unavailable | unsatisfactory | entered-in-error
    Comments

    This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid.

    Control0..1
    BindingThe codes SHALL be taken from SpecimenStatushttp://hl7.org/fhir/ValueSet/specimen-status|4.0.1
    (required to http://hl7.org/fhir/ValueSet/specimen-status|4.0.1)

    Codes providing the status/availability of a specimen.

    Typecode
    Is Modifiertrue because 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
    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
    Summarytrue
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    18. Specimen.type
    Definition

    The kind of material that forms the specimen.

    ShortKind of material that forms the specimen
    Comments

    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.

    Control0..1
    BindingFor example codes, see hl7VS-specimenTypehttp://terminology.hl7.org/ValueSet/v2-0487
    (example to http://terminology.hl7.org/ValueSet/v2-0487)

    The type of the specimen.

    TypeCodeableConcept
    Is Modifierfalse
    Must Supporttrue
    Summarytrue
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    20. Specimen.subject
    Definition

    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.

    ShortWhere 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
    Control10..1
    TypeReference(Botswana Patient, Patient, Group, Device, Substance, Location)
    Is Modifierfalse
    Summarytrue
    Requirements

    Must know the subject context.

    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    22. Specimen.receivedTime
    Definition

    Time when specimen was received for processing or testing.

    ShortThe time when specimen was received for processing
    Control0..1
    TypedateTime
    Is Modifierfalse
    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
    Must Supporttrue
    Summarytrue
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    24. Specimen.request
    Definition

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

    ShortWhy the specimen was collected
    Comments

    The request may be explicit or implied such with a ServiceRequest that requires a blood draw.

    Control10..*
    TypeReference(ServiceRequest - Lab Orders, ServiceRequest)
    Is Modifierfalse
    Summaryfalse
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    26. Specimen.collection
    Definition

    Details concerning the specimen collection.

    ShortCollection details
    Control10..1
    TypeBackboneElement
    Is Modifierfalse
    Summaryfalse
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    28. Specimen.collection.modifierExtension
    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).

    ShortExtensions that cannot be ignored even if unrecognized
    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.

    Control0..*
    TypeExtension
    Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
    Summarytrue
    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.

    Alternate Namesextensions, user content, modifiers
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
    30. Specimen.collection.collected[x]
    Definition

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

    ShortCollection time
    Control10..1
    TypedateTime, Period
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    Is Modifierfalse
    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
    Summarytrue
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    32. Specimen.collection.fastingStatus[x]
    Definition

    Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection.

    ShortWhether or how long patient abstained from food and/or drink
    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).

    Control0..1
    BindingUnless not suitable, these codes SHALL be taken from hl7VS-relevantClincialInformationhttp://terminology.hl7.org/ValueSet/v2-0916
    (extensible to http://terminology.hl7.org/ValueSet/v2-0916)

    Codes describing the fasting status of the patient.

    TypeChoice of: CodeableConcept, Duration
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    Is Modifierfalse
    Summarytrue
    Requirements

    Many diagnostic tests require fasting to facilitate accurate interpretation.

    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    SlicingThis element introduces a set of slices on Specimen.collection.fastingStatus[x]. The slices areUnordered and Open, and can be differentiated using the following discriminators:
    • type @ $this
    • 34. Specimen.collection.fastingStatus[x]:fastingStatusCodeableConcept
      Slice NamefastingStatusCodeableConcept
      Definition

      Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection.

      ShortWhether or how long patient abstained from food and/or drink
      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).

      Control0..1
      BindingThe codes SHALL be taken from Unless not suitable, these codes SHALL be taken from http://terminology.hl7.org/ValueSet/v2-0916|2.9
      (required to http://terminology.hl7.org/ValueSet/v2-0916|2.9)
      TypeCodeableConcept, Duration
      [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
      Is Modifierfalse
      Summarytrue
      Requirements

      Many diagnostic tests require fasting to facilitate accurate interpretation.

      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      36. Specimen.condition
      Definition

      A mode or state of being that describes the nature of the specimen.

      ShortState of the specimen
      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.

      Control0..*
      BindingThe codes SHALL be taken from Unless not suitable, these codes SHALL be taken from v2.0493 (2.9) .http://terminology.hl7.org/ValueSet/v2-0493
      (required to http://terminology.hl7.org/ValueSet/v2-0493|2.9)
      TypeCodeableConcept
      Is Modifierfalse
      Summarytrue
      Requirements

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

      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))