# US Core Specimen Profile - US Core Implementation Guide v9.0.0

* [**Table of Contents**](toc.md)
* [**Artifacts Summary**](artifacts.md)
* **US Core Specimen Profile**

## Resource Profile: US Core Specimen Profile 

| | | |
| :--- | :--- | :--- |
| *Official URL*:http://hl7.org/fhir/us/core/StructureDefinition/us-core-specimen | *Version*:9.0.0 | |
| * Standards status: *[Trial-use](http://hl7.org/fhir/R4/versions.html#std-process) | [Maturity Level](changes-between-versions.md#us-core-maturity-levels): 3 | *Computable Name*:USCoreSpecimenProfile |
| *Other Identifiers:*OID:2.16.840.1.113883.4.642.40.2.42.64 | | |

 
The US Core Specimen Profile inherits from the FHIR [Specimen](https://hl7.org/fhir/R4/specimen.html) 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:

* Query for a patient's specimen
* [Record or update](us-core-roadmap.md#future-candidate-requirements-under-consideration) a specimen for a patient

### Mandatory and Must Support Data Elements

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

**Each Specimen Must Have:**

1. a specimen type code1

**Each Specimen Must Support:**

1. business identifier(s)2
1. an accession identifier2
1. a patient

**Additional USCDI Requirements:**

These [Additional USCDI Requirements](must-support.md#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
1. specimen condition3

1,2,3 see guidance below

### Profile Specific Implementation Guidance

This section provides detailed implementation guidance for the US Core Profile to support implementation and certification.

* 1Since the binding is [extensible](http://hl7.org/fhir/R4/terminologies.html#extensible) when a code is unavailable, servers **MAY** use text.[§](requirements.md#CONF-0523)
* 1Although 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.[§](requirements.md#CONF-0524) 
* The Client application **SHALL** support both elements.[§](requirements.md#CONF-0525)
 
* 3The 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 can request Specimen resources be included with the Observation or DiagnosticReport resource query. An example query is provided in the [Notes](#notes) section below.

**Usages:**

* Refer to this Profile: [US Core Laboratory Result Observation Profile](StructureDefinition-us-core-observation-lab.md)
* Examples for this Profile: [Specimen/example-serum-lipemic](Specimen-example-serum-lipemic.md), [Specimen/specimen-example-serum](Specimen-specimen-example-serum.md), [Specimen/specimen-example-urine](Specimen-specimen-example-urine.md) and [Specimen/specimen-example-whole-blood](Specimen-specimen-example-whole-blood.md)
* CapabilityStatements using this Profile: [US Core Client CapabilityStatement](CapabilityStatement-us-core-client.md) and [US Core Server CapabilityStatement](CapabilityStatement-us-core-server.md)

You can also check for [usages in the FHIR IG Statistics](https://packages2.fhir.org/xig/resource/hl7.fhir.us.core|current/StructureDefinition/StructureDefinition-us-core-specimen.json)

**Changes since version 8.0.1:**

* The resource metadata has changed (copyright)

### Formal Views of Profile Content

 [Description of Profiles, Differentials, Snapshots and how the different presentations work](http://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#structure-definitions). 

 

Other representations of profile: [CSV](StructureDefinition-us-core-specimen.csv), [Excel](StructureDefinition-us-core-specimen.xlsx), [Schematron](StructureDefinition-us-core-specimen.sch) 

### 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](CapabilityStatement-us-core-server.md) for a complete list of supported RESTful interactions for this IG.

* See the [Scopes Format](scopes.md#scopes-format) section for a description of the SMART scopes syntax.
* See the [Search Syntax](general-guidance.md#search-syntax) section for a description of the US Core search syntax.
* See the [General Requirements](general-requirements.md) section for additional rules and expectations when a Server requires status parameters.
* See the [General Guidance](general-guidance.md) 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](scopes.md#smart-scopes):

* [resource level scopes](http://hl7.org/fhir/smart-app-launch/STU2.2/scopes-and-launch-context.html#scopes-for-requesting-clinical-data): `<patient|user|system>/Specimen.rs` [§](requirements.md#CONF-0155)

-------

#### 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](SearchParameter-us-core-specimen-id.md) search parameter`GET [base]/Specimen?_id=[id]' or 'GET [base]/Specimen/[id]`Example:
> 
1. GET [base]/Specimen?_id=123

**Implementation Notes**: (see [Parameters for all resources](http://hl7.org/fhir/R4/search.html#token)).

#### Optional Search Parameters:

The following search parameters and search parameter combinations **SHOULD** be supported

1. **SHOULD** support searching for all specimen's for a patient using the [patient](SearchParameter-us-core-specimen-patient.md) search parameter`GET [base]/Specimen?patient={Patient/}[id]`Example:
> 
1. GET [base]/Specimen?patient=1137192

**Implementation Notes**: Fetches a bundle of all US Core Specimen Profile resources for the specified patient ( see [how to search by reference](http://hl7.org/fhir/R4/search.html#reference)).

#### Including Specimen when searching for an Observation or DiagnosticReport

Servers **MAY** support the [`_include`](http://hl7.org/fhir/R4/search.html#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



## Resource Content

```json
{
  "resourceType" : "StructureDefinition",
  "id" : "us-core-specimen",
  "extension" : [{
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
    "valueInteger" : 3
  },
  {
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
    "valueCode" : "cgp"
  },
  {
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
    "valueCode" : "trial-use",
    "_valueCode" : {
      "extension" : [{
        "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
        "valueCanonical" : "http://hl7.org/fhir/us/core/ImplementationGuide/hl7.fhir.us.core"
      }]
    }
  }],
  "url" : "http://hl7.org/fhir/us/core/StructureDefinition/us-core-specimen",
  "identifier" : [{
    "system" : "urn:ietf:rfc:3986",
    "value" : "urn:oid:2.16.840.1.113883.4.642.40.2.42.64"
  }],
  "version" : "9.0.0",
  "name" : "USCoreSpecimenProfile",
  "title" : "US Core Specimen Profile",
  "status" : "active",
  "experimental" : false,
  "date" : "2023-10-17",
  "publisher" : "HL7 International / Cross-Group Projects",
  "contact" : [{
    "name" : "HL7 International / Cross-Group Projects",
    "telecom" : [{
      "system" : "url",
      "value" : "http://www.hl7.org/Special/committees/cgp"
    },
    {
      "system" : "email",
      "value" : "cgp@lists.HL7.org"
    }]
  }],
  "description" : "The US Core Specimen Profile inherits from the FHIR [Specimen](https://hl7.org/fhir/R4/specimen.html) 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.",
  "jurisdiction" : [{
    "coding" : [{
      "system" : "urn:iso:std:iso:3166",
      "code" : "US"
    }]
  }],
  "fhirVersion" : "4.0.1",
  "mapping" : [{
    "identity" : "rim",
    "uri" : "http://hl7.org/v3",
    "name" : "RIM Mapping"
  },
  {
    "identity" : "w5",
    "uri" : "http://hl7.org/fhir/fivews",
    "name" : "FiveWs Pattern Mapping"
  },
  {
    "identity" : "v2",
    "uri" : "http://hl7.org/v2",
    "name" : "HL7 v2 Mapping"
  }],
  "kind" : "resource",
  "abstract" : false,
  "type" : "Specimen",
  "baseDefinition" : "http://hl7.org/fhir/StructureDefinition/Specimen",
  "derivation" : "constraint",
  "differential" : {
    "element" : [{
      "id" : "Specimen",
      "path" : "Specimen",
      "mustSupport" : false
    },
    {
      "id" : "Specimen.identifier",
      "path" : "Specimen.identifier",
      "short" : "Specimen identifier",
      "mustSupport" : true
    },
    {
      "id" : "Specimen.accessionIdentifier",
      "path" : "Specimen.accessionIdentifier",
      "mustSupport" : true
    },
    {
      "id" : "Specimen.type",
      "path" : "Specimen.type",
      "min" : 1,
      "mustSupport" : true,
      "binding" : {
        "strength" : "extensible",
        "valueSet" : "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54"
      }
    },
    {
      "id" : "Specimen.subject",
      "path" : "Specimen.subject",
      "short" : "The patient where the specimen came from.",
      "type" : [{
        "code" : "Reference",
        "targetProfile" : ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient",
        "http://hl7.org/fhir/StructureDefinition/Group",
        "http://hl7.org/fhir/us/core/StructureDefinition/us-core-device",
        "http://hl7.org/fhir/StructureDefinition/Substance",
        "http://hl7.org/fhir/us/core/StructureDefinition/us-core-location"],
        "_targetProfile" : [{
          "extension" : [{
            "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support",
            "valueBoolean" : true
          }]
        },
        {
          "extension" : [{
            "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support",
            "valueBoolean" : false
          }]
        },
        {
          "extension" : [{
            "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support",
            "valueBoolean" : false
          }]
        },
        {
          "extension" : [{
            "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support",
            "valueBoolean" : false
          }]
        },
        {
          "extension" : [{
            "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support",
            "valueBoolean" : false
          }]
        }]
      }],
      "mustSupport" : true
    },
    {
      "id" : "Specimen.collection",
      "extension" : [{
        "url" : "http://hl7.org/fhir/us/core/StructureDefinition/uscdi-requirement",
        "valueBoolean" : true
      }],
      "path" : "Specimen.collection",
      "short" : "𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜: Collection details"
    },
    {
      "id" : "Specimen.collection.bodySite",
      "extension" : [{
        "url" : "http://hl7.org/fhir/us/core/StructureDefinition/uscdi-requirement",
        "valueBoolean" : true
      }],
      "path" : "Specimen.collection.bodySite",
      "short" : "𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜: Specimen Source Site",
      "comment" : "Body location from where a specimen was obtained. Examples include but are not limited to right internal jugular, left arm, and right eye.",
      "binding" : {
        "strength" : "extensible",
        "valueSet" : "http://hl7.org/fhir/ValueSet/body-site"
      }
    },
    {
      "id" : "Specimen.condition",
      "extension" : [{
        "url" : "http://hl7.org/fhir/us/core/StructureDefinition/uscdi-requirement",
        "valueBoolean" : true
      }],
      "path" : "Specimen.condition",
      "short" : "𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜: Specimen condition",
      "binding" : {
        "strength" : "extensible",
        "valueSet" : "http://hl7.org/fhir/us/core/ValueSet/us-core-specimen-condition"
      }
    }]
  }
}

```
