US Core Implementation Guide
8.0.0 - STU 8 United States of America flag

US Core Implementation Guide, published by HL7 International / Cross-Group Projects. This guide is not an authorized publication; it is the continuous build for version 8.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/US-Core/ and changes regularly. See the Directory of published versions

Resource Profile: US Core Specimen Profile

Official URL: http://hl7.org/fhir/us/core/StructureDefinition/us-core-specimen Version: 8.0.0
Standards status: Trial-use Computable Name: USCoreSpecimenProfile
Other Identifiers: OID:2.16.840.1.113883.4.642.40.2.42.63

Copyright/Legal: Used by permission of HL7 International, all rights reserved Creative Commons License

The US Core Specimen Profile inherits from the FHIR Specimen resource; refer to it for scope and usage definitions. This profile sets minimum expectations for the Specimen resource to record, search, and fetch information about substances associated with a patient being sampled or tested (such as nasopharyngeal swab, whole blood, or serum). It specifies which core elements, extensions, vocabularies, and value sets SHALL be present and constrains how the elements are used. Providing the floor for standards development for specific use cases promotes interoperability and adoption.

Example Usage Scenarios:

The following are example usage scenarios for the US Core Specimen profile:

Mandatory and Must Support Data Elements

The following data elements must always be present (Mandatory definition) or must be supported if the data is present in the sending system (Must Support definition). They are presented below in a simple human-readable explanation. Profile specific guidance and examples are provided as well. The Formal Views below provides the formal summary, definitions, and terminology requirements.

Each Specimen Must Have:

  1. a specimen code

Each Specimen Must Support:

  1. business identifier(s)*
  2. an accession identifier*
  3. a patient

Additional USCDI Requirements:

These Additional USCDI Requirements elements are not Mandatory or Must Support but are required for ONC Health IT certification testing and are included in the formal definition of the profile and the Specimen examples.

  1. specimen collection source site
  2. specimen condition*

* see guidance below

Profile Specific Implementation Guidance:

  • Since the binding is extensible when a code is unavailable, just text is allowed.
  • *Although both Specimen.identifier and Specimen.accessionIdentifier are marked as Must Support, the Server system is not required to support both, but SHALL support at least one of these elements.
    • The Client application SHALL support both elements.
  • *The specimen condition is used by the laboratory to determine the acceptability of a specimen for the ordered test. An individual specimen condition may be acceptable for one test and not for another. The specimen condition is typically provided when the specimen does not meet the laboratory's criteria for acceptability, whether the test was performed or not. Examples include but are not limited to hemolyzed, clotted, container leaking, and missing patient names. This element may include information about the contents of the container, the container, and the label.
  • in addition to Specimen search criteria, Clients may request Specimen resources be included with the Observation or DiagnosticReport resource query. An example query is provided in the Notes section below.

Usage:

Changes since version 7.0.0:

  • The data elements list has changed

    • Formal Views of Profile Content

    Description of Profiles, Differentials, Snapshots and how the different presentations work.

    NameFlagsCard.TypeDescription & Constraintsdoco
    .. Specimen 0..* Specimen Sample for analysis
    dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources
    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
    dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
    dom-5: If a resource is contained in another resource, it SHALL NOT have a security label
    dom-6: A resource should have narrative for robust management
    ... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
    ele-1: All FHIR elements must have a @value or children
    ... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
    ele-1: All FHIR elements must have a @value or children
    ext-1: Must have either extensions or value[x], not both
    ... identifier SΣ 0..* Identifier Specimen identifier
    ele-1: All FHIR elements must have a @value or children
    ... accessionIdentifier SΣ 0..1 Identifier Identifier assigned by the lab
    ele-1: All FHIR elements must have a @value or children
    ... status ?!Σ 0..1 code available | unavailable | unsatisfactory | entered-in-error
    Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.


    ele-1: All FHIR elements must have a @value or children
    ... type SΣ 1..1 CodeableConcept Kind of material that forms the specimen
    Binding: Specimen type . (extensible)
    ele-1: All FHIR elements must have a @value or children
    ... subject SΣ 0..1 Reference(US Core Patient Profile) The patient where the specimen came from.
    ele-1: All FHIR elements must have a @value or children
    ... collection 0..1 BackboneElement 𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜: Collection details
    ele-1: All FHIR elements must have a @value or children
    .... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
    ele-1: All FHIR elements must have a @value or children
    ext-1: Must have either extensions or value[x], not both
    .... bodySite 0..1 CodeableConcept 𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜: Specimen Source Site
    Binding: SNOMEDCTBodyStructures (extensible)
    ele-1: All FHIR elements must have a @value or children
    ... condition Σ 0..* CodeableConcept 𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜: Specimen condition
    Binding: US Core Specimen Condition (extensible)
    ele-1: All FHIR elements must have a @value or children

    doco Documentation for this format

    Terminology Bindings

    PathConformanceValueSetURI
    Specimen.statusrequiredSpecimenStatus
    http://hl7.org/fhir/ValueSet/specimen-status|4.0.1
    from the FHIR Standard
    Specimen.typeextensibleSpecimenType .
    http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54
    Specimen.collection.bodySiteextensibleSNOMEDCTBodyStructures
    http://hl7.org/fhir/ValueSet/body-site
    from the FHIR Standard
    Specimen.conditionextensibleUSCoreSpecimenCondition
    http://hl7.org/fhir/us/core/ValueSet/us-core-specimen-condition
    from this IG

     

    Other representations of profile: CSV, Excel, Schematron

    Notes:

    Quick Start

    Below is an overview of the required Server RESTful FHIR interactions for this profile - for example, search and read operations - when supporting the US Core interactions to access this profile's information (Profile Support + Interaction Support). Note that systems that support only US Core Profiles (Profile Only Support) are not required to support these interactions. See the US Core Server CapabilityStatement for a complete list of supported RESTful interactions for this IG.

    • See the Scopes Format section for a description of the SMART scopes syntax.
    • See the Search Syntax section for a description of the US Core search syntax.
    • See the General Requirements section for additional rules and expectations when a Server requires status parameters.
    • See the General Guidance section for additional guidance on searching for multiple patients.

    US Core Scopes

    Servers providing access to specimen data SHALL support these US Core SMART Scopes:

    Mandatory Search Parameters:

    The following search parameters and search parameter combinations SHALL be supported:

    1. SHALL support both read Specimen by id AND Specimen search using the _id search parameter:

      GET [base]/Specimen/[id] or GET [base]/Specimen?_id=[id]

      Example:

      1. GET [base]/Specimen?_id=123

      Implementation Notes: (how to search by the logical id of the resource)

    Optional Search Parameters:

    The following search parameter combinations SHOULD be supported:

    1. SHOULD support searching for all specimens for a patient using the patient search parameter:

      GET [base]/Specimen?patient={Type/}[id]

      Example:

      1. GET [base]/Specimen?patient=1137192

      Implementation Notes: Fetches a bundle of all Specimen resources for the specified patient (how to search by reference)

    Including Specimen when searching for an Observation or DiagnosticReport

    Servers MAY support the _include parameter to request that additional resources be included in the response of a search query. For example, when searching for an Observation or DiagnosticReport that references Specimen, the Client can use the _include parameter to retrieve information about a specimen associated with the search results. The syntax for querying an Observation and the associated Specimen is:

    GET [base]/[Resource-type]?[parameter1]=[value1]{&...}&_include=Observation:specimen

    Example:

    GET [base]/Observation?_id=9163726&_include=Observation:specimen