Botswana FHIR Implementation Guide - Laboratory
1.0.0 - STU1 Botswana flag

Botswana FHIR Implementation Guide - Laboratory, 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/bw-laboratory-workflows-ig/ and changes regularly. See the Directory of published versions

Resource Profile: PimsUATSpecimen - Detailed Descriptions

Active as of 2024-08-28

Definitions for the uat-pims-specimen resource profile.

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

0. Specimen
2. Specimen.request
TypeReference(Service Request - PIMS Lab Orders)

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.

    Control10..1
    BindingUnless not suitable, these codes SHALL be taken from For example codes, see Specimen Type Used In Viral Load testinghttp://terminology.hl7.org/ValueSet/v2-0487
    (extensible to http://moh.bw.org/ValueSet/vs-specimen-type)
    TypeCodeableConcept
    Is Modifierfalse
    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(Patient - PIMS, Patient - OpenMRS, 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
    Control10..1
    TypedateTime
    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()))
    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(Service Request - PIMS 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()))

    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.id
    Definition

    The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.

    ShortLogical id of this artifact
    Comments

    The only time that a resource does not have an id is when it is being submitted to the server using a create operation.

    Control0..1
    Typeid
    Is Modifierfalse
    Summarytrue
    4. Specimen.meta
    Definition

    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.

    ShortMetadata about the resource
    Control0..1
    TypeMeta
    Is Modifierfalse
    Summarytrue
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    6. 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()))
    8. Specimen.language
    Definition

    The base language in which the resource is written.

    ShortLanguage of the resource content
    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).

    Control0..1
    BindingThe codes SHOULD be taken from CommonLanguages
    (preferred to http://hl7.org/fhir/ValueSet/languages)

    A human language.

    Additional BindingsPurpose
    AllLanguagesMax Binding
    Typecode
    Is Modifierfalse
    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
    Summaryfalse
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    10. Specimen.text
    Definition

    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.

    ShortText summary of the 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.

    Control0..1
    TypeNarrative
    Is Modifierfalse
    Summaryfalse
    Alternate Namesnarrative, html, xhtml, display
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    12. Specimen.contained
    Definition

    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.

    ShortContained, inline Resources
    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.

    Control0..*
    TypeResource
    Is Modifierfalse
    Summaryfalse
    Alternate Namesinline resources, anonymous resources, contained resources
    14. Specimen.extension
    Definition

    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.

    ShortAdditional content defined by implementations
    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 Modifierfalse
    Summaryfalse
    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())
    16. 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())
    18. Specimen.identifier
    Definition

    reasons why this should be supported

    ShortExternal Identifier
    NoteThis is a business identifier, not a resource identifier (see discussion)
    Control1..*
    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
    • 20. Specimen.identifier:USID
      Slice NameUSID
      Definition

      Id for specimen.

      ShortExternal Identifier
      NoteThis is a business identifier, not a resource identifier (see discussion)
      Control1..1
      TypeIdentifier
      Is Modifierfalse
      Summarytrue
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      22. Specimen.identifier:USID.id
      Definition

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

      ShortUnique id for inter-element referencing
      Control0..1
      Typestring
      Is Modifierfalse
      XML FormatIn the XML format, this property is represented as an attribute.
      Summaryfalse
      24. Specimen.identifier:USID.extension
      Definition

      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.

      ShortAdditional content defined by implementations
      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 Modifierfalse
      Summaryfalse
      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())
      SlicingThis element introduces a set of slices on Specimen.identifier.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
      • value @ url
      • 26. 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 IdentifierUse
        (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()))
        28. Specimen.identifier:USID.type
        Definition

        A coded type for the identifier that can be used to determine which identifier to use for a specific purpose.

        ShortDescription of identifier
        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.

        Control0..1
        BindingUnless not suitable, these codes SHALL be taken from Identifier Type Codes
        (extensible to http://hl7.org/fhir/ValueSet/identifier-type)

        A coded type for an identifier that can be used to determine which identifier to use for a specific purpose.

        TypeCodeableConcept
        Is Modifierfalse
        Summarytrue
        Requirements

        Allows users to make use of identifiers when the identifier system is not known.

        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        30. 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.

        Control1..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()))
        32. 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.

        Control1..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()))
        34. Specimen.identifier:USID.period
        Definition

        Time period during which identifier is/was valid for use.

        ShortTime period when id is/was valid for use
        Control0..1
        TypePeriod
        Is Modifierfalse
        Summarytrue
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        36. Specimen.identifier:USID.assigner
        Definition

        Organization that issued/manages the identifier.

        ShortOrganization that issued id (may be just text)
        Comments

        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.

        Control0..1
        TypeReference(Organization)
        Is Modifierfalse
        Summarytrue
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        38. Specimen.accessionIdentifier
        Definition

        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.

        ShortIdentifier assigned by the lab
        Control0..1
        TypeIdentifier
        Is Modifierfalse
        Summarytrue
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        40. 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 SpecimenStatus
        (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()))
        42. 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.

        Control1..1
        BindingUnless not suitable, these codes SHALL be taken from Specimen Type Used In Viral Load testing
        (extensible to http://moh.bw.org/ValueSet/vs-specimen-type)
        TypeCodeableConcept
        Is Modifierfalse
        Summarytrue
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        44. 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
        Control1..1
        TypeReference(Patient - PIMS, Patient - OpenMRS)
        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()))
        46. Specimen.receivedTime
        Definition

        Time when specimen was received for processing or testing.

        ShortThe time when specimen was received for processing
        Control1..1
        TypedateTime
        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()))
        48. Specimen.parent
        Definition

        Reference to the parent (source) specimen which is used when the specimen was either derived from or a component of another specimen.

        ShortSpecimen from which this specimen originated
        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.

        Control0..*
        TypeReference(Specimen)
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        50. 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.

        Control1..*
        TypeReference(Service Request - PIMS Lab Orders)
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        52. Specimen.collection
        Definition

        Details concerning the specimen collection.

        ShortCollection details
        Control1..1
        TypeBackboneElement
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        54. Specimen.collection.id
        Definition

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

        ShortUnique id for inter-element referencing
        Control0..1
        Typestring
        Is Modifierfalse
        XML FormatIn the XML format, this property is represented as an attribute.
        Summaryfalse
        56. Specimen.collection.extension
        Definition

        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.

        ShortAdditional content defined by implementations
        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 Modifierfalse
        Summaryfalse
        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())
        58. 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())
        60. Specimen.collection.collector
        Definition

        Person who collected the specimen.

        ShortWho collected the specimen
        Control0..1
        TypeReference(Practitioner, PractitionerRole)
        Is Modifierfalse
        Summarytrue
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        62. Specimen.collection.collected[x]
        Definition

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

        ShortCollection time
        Control1..1
        TypedateTime
        [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()))
        64. Specimen.collection.duration
        Definition

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

        ShortHow long it took to collect specimen
        Control0..1
        TypeDuration
        Is Modifierfalse
        Summarytrue
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        66. Specimen.collection.quantity
        Definition

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

        ShortThe quantity of specimen collected
        Control0..1
        TypeQuantity(SimpleQuantity)
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        68. Specimen.collection.method
        Definition

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

        ShortTechnique used to perform collection
        Control0..1
        BindingFor example codes, see FHIRSpecimenCollectionMethod
        (example to http://hl7.org/fhir/ValueSet/specimen-collection-method)

        The technique that is used to perform the procedure.

        TypeCodeableConcept
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        70. Specimen.collection.bodySite
        Definition

        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.

        ShortAnatomical collection site
        Comments

        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.

        Control0..1
        BindingFor example codes, see SNOMEDCTBodyStructures
        (example to http://hl7.org/fhir/ValueSet/body-site)

        Codes describing anatomical locations. May include laterality.

        TypeCodeableConcept
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        72. 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-relevantClincialInformation
        (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()))
        74. Specimen.processing
        Definition

        Details concerning processing and processing steps for the specimen.

        ShortProcessing and processing step details
        Control0..*
        TypeBackboneElement
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        76. Specimen.processing.id
        Definition

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

        ShortUnique id for inter-element referencing
        Control0..1
        Typestring
        Is Modifierfalse
        XML FormatIn the XML format, this property is represented as an attribute.
        Summaryfalse
        78. Specimen.processing.extension
        Definition

        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.

        ShortAdditional content defined by implementations
        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 Modifierfalse
        Summaryfalse
        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())
        80. Specimen.processing.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())
        82. Specimen.processing.description
        Definition

        Textual description of procedure.

        ShortTextual description of procedure
        Control0..1
        Typestring
        Is Modifierfalse
        Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        84. Specimen.processing.procedure
        Definition

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

        ShortIndicates the treatment step applied to the specimen
        Control0..1
        BindingFor example codes, see SpecimenProcessingProcedure
        (example to http://hl7.org/fhir/ValueSet/specimen-processing-procedure)

        Type indicating the technique used to process the specimen.

        TypeCodeableConcept
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        86. Specimen.processing.additive
        Definition

        Material used in the processing step.

        ShortMaterial used in the processing step
        Control0..*
        TypeReference(Substance)
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        88. Specimen.processing.time[x]
        Definition

        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.

        ShortDate and time of specimen processing
        Control0..1
        TypeChoice of: dateTime, 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
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        90. Specimen.container
        Definition

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

        ShortDirect container of specimen (tube/slide, etc.)
        Control0..*
        TypeBackboneElement
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        92. Specimen.container.id
        Definition

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

        ShortUnique id for inter-element referencing
        Control0..1
        Typestring
        Is Modifierfalse
        XML FormatIn the XML format, this property is represented as an attribute.
        Summaryfalse
        94. Specimen.container.extension
        Definition

        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.

        ShortAdditional content defined by implementations
        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 Modifierfalse
        Summaryfalse
        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())
        96. Specimen.container.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())
        98. Specimen.container.identifier
        Definition

        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.

        ShortId for the container
        NoteThis is a business identifier, not a resource identifier (see discussion)
        Control0..*
        TypeIdentifier
        Is Modifierfalse
        Summarytrue
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        100. Specimen.container.description
        Definition

        Textual description of the container.

        ShortTextual description of the container
        Control0..1
        Typestring
        Is Modifierfalse
        Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        102. Specimen.container.type
        Definition

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

        ShortKind of container directly associated with specimen
        Control0..1
        BindingFor example codes, see SpecimenContainerType
        (example to http://hl7.org/fhir/ValueSet/specimen-container-type)

        Type of specimen container.

        TypeCodeableConcept
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        104. Specimen.container.capacity
        Definition

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

        ShortContainer volume or size
        Control0..1
        TypeQuantity(SimpleQuantity)
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        106. Specimen.container.specimenQuantity
        Definition

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

        ShortQuantity of specimen within container
        Control0..1
        TypeQuantity(SimpleQuantity)
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        108. Specimen.container.additive[x]
        Definition

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

        ShortAdditive associated with container
        Control0..1
        BindingFor example codes, see hl7VS-additivePreservative
        (example to http://terminology.hl7.org/ValueSet/v2-0371)

        Substance added to specimen container.

        TypeChoice of: CodeableConcept, Reference(Substance)
        [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        110. 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..*
        BindingUnless not suitable, these codes SHALL be taken from hl7VS-specimenCondition
        (extensible to http://terminology.hl7.org/ValueSet/v2-0493)

        Codes describing the state of the specimen.

        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()))
        112. Specimen.note
        Definition

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

        ShortComments
        Control0..*
        TypeAnnotation
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))