UK Core Implementation Guide STU3 Sequence - Sprint 6 Review

StructureDefinition-UKCore-Specimen

Description

This profile defines the UK constraints and extensions on the International FHIR resource Specimen.

Profile Purpose

This profile allows exchange of information about a sample to be used for analysis.

Snapshot View

statusΣ ?!0..1codeBinding
receivedTimeΣ0..1dateTime
conditionΣ0..*CodeableConceptBinding

Differential View

Hybrid View

statusΣ ?!0..1codeBinding
receivedTimeΣ0..1dateTime
conditionΣ0..*CodeableConceptBinding

Table View

Specimen..
Specimen.identifier..
Specimen.identifier.assignerReference(UK Core Organization)..
Specimen.accessionIdentifier..
Specimen.accessionIdentifier.assignerReference(UK Core Organization)..
Specimen.type..
Specimen.type.coding..
Specimen.type.coding..
Specimen.type.coding.system1..
Specimen.type.coding.code1..
Specimen.type.coding.display1..
Specimen.subjectReference(Group | UK Core Device | Substance | UK Core Patient | UK Core Location)..
Specimen.subject.identifier..
Specimen.subject.identifier.assignerReference(UK Core Organization)..
Specimen.parentReference(UK Core Specimen)..
Specimen.parent.identifier..
Specimen.parent.identifier.assignerReference(UK Core Organization)..
Specimen.requestReference(UK Core ServiceRequest)..
Specimen.request.identifier..
Specimen.request.identifier.assignerReference(UK Core Organization)..
Specimen.collection..
Specimen.collection.collectorReference(UK Core Practitioner | UK Core PractitionerRole)..
Specimen.collection.collector.identifier..
Specimen.collection.collector.identifier.assignerReference(UK Core Organization)..
Specimen.collection.bodySite..
Specimen.collection.bodySite.coding..
Specimen.collection.bodySite.coding..1
Specimen.collection.bodySite.coding.system1..
Specimen.collection.bodySite.coding.code1..
Specimen.collection.bodySite.coding.display1..
Specimen.processing..
Specimen.processing.additive..
Specimen.processing.additive.identifier..
Specimen.processing.additive.identifier.assignerReference(UK Core Organization)..
Specimen.container..
Specimen.container.identifier..
Specimen.container.identifier.assignerReference(UK Core Organization)..
Specimen.note..
Specimen.note.author[x]Reference(UK Core Patient | UK Core Practitioner | UK Core RelatedPerson | UK Core Organization), string..


XML View

<StructureDefinition xmlns="http://hl7.org/fhir">
    <id value="UKCore-Specimen" />
    <url value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Specimen" />
    <version value="2.2.0" />
    <name value="UKCoreSpecimen" />
    <title value="UK Core Specimen" />
    <status value="draft" />
    <date value="2023-02-14" />
    <publisher value="HL7 UK" />
    <contact>
        <name value="HL7 UK" />
        <telecom>
            <system value="email" />
            <value value="ukcore@hl7.org.uk" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <description value="This profile defines the UK constraints and extensions on the International FHIR resource [Specimen](https://hl7.org/fhir/R4/Specimen.html)." />
    <purpose value="This profile allows exchange of information about a sample to be used for analysis." />
    <copyright value="Copyright &#169; 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License. You may obtain a copy of the License at  http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an &quot;AS IS&quot; BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7&#174; FHIR&#174; standard Copyright &#169; 2011+ HL7 The HL7&#174; FHIR&#174; standard is used under the FHIR license. You may obtain a copy of the FHIR license at  https://www.hl7.org/fhir/license.html." />
    <fhirVersion value="4.0.1" />
    <mapping>
        <identity value="rim" />
        <uri value="http://hl7.org/v3" />
        <name value="RIM Mapping" />
    </mapping>
    <mapping>
        <identity value="w5" />
        <uri value="http://hl7.org/fhir/fivews" />
        <name value="FiveWs Pattern Mapping" />
    </mapping>
    <mapping>
        <identity value="v2" />
        <uri value="http://hl7.org/v2" />
        <name value="HL7 v2 Mapping" />
    </mapping>
    <kind value="resource" />
    <abstract value="false" />
    <type value="Specimen" />
    <baseDefinition value="http://hl7.org/fhir/StructureDefinition/Specimen" />
    <derivation value="constraint" />
    <differential>
        <element id="Specimen.identifier.assigner">
            <path value="Specimen.identifier.assigner" />
            <type>
                <code value="Reference" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization" />
            </type>
        </element>
        <element id="Specimen.accessionIdentifier.assigner">
            <path value="Specimen.accessionIdentifier.assigner" />
            <type>
                <code value="Reference" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization" />
            </type>
        </element>
        <element id="Specimen.type.coding">
            <path value="Specimen.type.coding" />
            <slicing>
                <discriminator>
                    <type value="value" />
                    <path value="system" />
                </discriminator>
                <rules value="open" />
            </slicing>
        </element>
        <element id="Specimen.type.coding:snomedCT">
            <path value="Specimen.type.coding" />
            <sliceName value="snomedCT" />
            <binding>
                <strength value="preferred" />
                <description value="A code from the SNOMED UK Clinical Terminology coding system" />
                <valueSet value="https://fhir.hl7.org.uk/ValueSet/UKCore-SpecimenType" />
            </binding>
        </element>
        <element id="Specimen.type.coding:snomedCT.system">
            <path value="Specimen.type.coding.system" />
            <min value="1" />
            <fixedUri value="http://snomed.info/sct" />
        </element>
        <element id="Specimen.type.coding:snomedCT.code">
            <path value="Specimen.type.coding.code" />
            <min value="1" />
        </element>
        <element id="Specimen.type.coding:snomedCT.display">
            <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable">
                <valueBoolean value="true" />
            </extension>
            <path value="Specimen.type.coding.display" />
            <min value="1" />
        </element>
        <element id="Specimen.subject">
            <path value="Specimen.subject" />
            <type>
                <code value="Reference" />
                <targetProfile value="http://hl7.org/fhir/StructureDefinition/Group" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Device" />
                <targetProfile value="http://hl7.org/fhir/StructureDefinition/Substance" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Location" />
            </type>
        </element>
        <element id="Specimen.subject.identifier.assigner">
            <path value="Specimen.subject.identifier.assigner" />
            <type>
                <code value="Reference" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization" />
            </type>
        </element>
        <element id="Specimen.parent">
            <path value="Specimen.parent" />
            <type>
                <code value="Reference" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Specimen" />
            </type>
        </element>
        <element id="Specimen.parent.identifier.assigner">
            <path value="Specimen.parent.identifier.assigner" />
            <type>
                <code value="Reference" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization" />
            </type>
        </element>
        <element id="Specimen.request">
            <path value="Specimen.request" />
            <type>
                <code value="Reference" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-ServiceRequest" />
            </type>
        </element>
        <element id="Specimen.request.identifier.assigner">
            <path value="Specimen.request.identifier.assigner" />
            <type>
                <code value="Reference" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization" />
            </type>
        </element>
        <element id="Specimen.collection.collector">
            <path value="Specimen.collection.collector" />
            <type>
                <code value="Reference" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Practitioner" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-PractitionerRole" />
            </type>
        </element>
        <element id="Specimen.collection.collector.identifier.assigner">
            <path value="Specimen.collection.collector.identifier.assigner" />
            <type>
                <code value="Reference" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization" />
            </type>
        </element>
        <element id="Specimen.collection.bodySite.coding">
            <path value="Specimen.collection.bodySite.coding" />
            <slicing>
                <discriminator>
                    <type value="value" />
                    <path value="system" />
                </discriminator>
                <rules value="open" />
            </slicing>
        </element>
        <element id="Specimen.collection.bodySite.coding:snomedCT">
            <path value="Specimen.collection.bodySite.coding" />
            <sliceName value="snomedCT" />
            <max value="1" />
            <binding>
                <strength value="preferred" />
                <description value="A code from the SNOMED UK Clinical Terminology coding system" />
                <valueSet value="https://fhir.hl7.org.uk/ValueSet/UKCore-SpecimenBodySite" />
            </binding>
        </element>
        <element id="Specimen.collection.bodySite.coding:snomedCT.system">
            <path value="Specimen.collection.bodySite.coding.system" />
            <min value="1" />
            <fixedUri value="http://snomed.info/sct" />
        </element>
        <element id="Specimen.collection.bodySite.coding:snomedCT.code">
            <path value="Specimen.collection.bodySite.coding.code" />
            <min value="1" />
        </element>
        <element id="Specimen.collection.bodySite.coding:snomedCT.display">
            <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable">
                <valueBoolean value="true" />
            </extension>
            <path value="Specimen.collection.bodySite.coding.display" />
            <min value="1" />
        </element>
        <element id="Specimen.processing.additive.identifier.assigner">
            <path value="Specimen.processing.additive.identifier.assigner" />
            <type>
                <code value="Reference" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization" />
            </type>
        </element>
        <element id="Specimen.container.identifier.assigner">
            <path value="Specimen.container.identifier.assigner" />
            <type>
                <code value="Reference" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization" />
            </type>
        </element>
        <element id="Specimen.note.author[x]">
            <path value="Specimen.note.author[x]" />
            <type>
                <code value="Reference" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Practitioner" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-RelatedPerson" />
                <targetProfile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization" />
            </type>
            <type>
                <code value="string" />
            </type>
        </element>
    </differential>
</StructureDefinition>

JSON View

{
    "resourceType": "StructureDefinition",
    "id": "UKCore-Specimen",
    "url": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Specimen",
    "version": "2.2.0",
    "name": "UKCoreSpecimen",
    "title": "UK Core Specimen",
    "status": "draft",
    "date": "2023-02-14",
    "publisher": "HL7 UK",
    "contact":  [
        {
            "name": "HL7 UK",
            "telecom":  [
                {
                    "system": "email",
                    "value": "ukcore@hl7.org.uk",
                    "use": "work",
                    "rank": 1
                }
            ]
        }
    ],
    "description": "This profile defines the UK constraints and extensions on the International FHIR resource [Specimen](https://hl7.org/fhir/R4/Specimen.html).",
    "purpose": "This profile allows exchange of information about a sample to be used for analysis.",
    "copyright": "Copyright © 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at  http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at  https://www.hl7.org/fhir/license.html.",
    "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.identifier.assigner",
                "path": "Specimen.identifier.assigner",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization"
                        ]
                    }
                ]
            },
            {
                "id": "Specimen.accessionIdentifier.assigner",
                "path": "Specimen.accessionIdentifier.assigner",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization"
                        ]
                    }
                ]
            },
            {
                "id": "Specimen.type.coding",
                "path": "Specimen.type.coding",
                "slicing": {
                    "discriminator":  [
                        {
                            "type": "value",
                            "path": "system"
                        }
                    ],
                    "rules": "open"
                }
            },
            {
                "id": "Specimen.type.coding:snomedCT",
                "path": "Specimen.type.coding",
                "sliceName": "snomedCT",
                "binding": {
                    "strength": "preferred",
                    "description": "A code from the SNOMED UK Clinical Terminology coding system",
                    "valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-SpecimenType"
                }
            },
            {
                "id": "Specimen.type.coding:snomedCT.system",
                "path": "Specimen.type.coding.system",
                "min": 1,
                "fixedUri": "http://snomed.info/sct"
            },
            {
                "id": "Specimen.type.coding:snomedCT.code",
                "path": "Specimen.type.coding.code",
                "min": 1
            },
            {
                "id": "Specimen.type.coding:snomedCT.display",
                "extension":  [
                    {
                        "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
                        "valueBoolean": true
                    }
                ],
                "path": "Specimen.type.coding.display",
                "min": 1
            },
            {
                "id": "Specimen.subject",
                "path": "Specimen.subject",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "http://hl7.org/fhir/StructureDefinition/Group",
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Device",
                            "http://hl7.org/fhir/StructureDefinition/Substance",
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient",
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Location"
                        ]
                    }
                ]
            },
            {
                "id": "Specimen.subject.identifier.assigner",
                "path": "Specimen.subject.identifier.assigner",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization"
                        ]
                    }
                ]
            },
            {
                "id": "Specimen.parent",
                "path": "Specimen.parent",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Specimen"
                        ]
                    }
                ]
            },
            {
                "id": "Specimen.parent.identifier.assigner",
                "path": "Specimen.parent.identifier.assigner",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization"
                        ]
                    }
                ]
            },
            {
                "id": "Specimen.request",
                "path": "Specimen.request",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-ServiceRequest"
                        ]
                    }
                ]
            },
            {
                "id": "Specimen.request.identifier.assigner",
                "path": "Specimen.request.identifier.assigner",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization"
                        ]
                    }
                ]
            },
            {
                "id": "Specimen.collection.collector",
                "path": "Specimen.collection.collector",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Practitioner",
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-PractitionerRole"
                        ]
                    }
                ]
            },
            {
                "id": "Specimen.collection.collector.identifier.assigner",
                "path": "Specimen.collection.collector.identifier.assigner",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization"
                        ]
                    }
                ]
            },
            {
                "id": "Specimen.collection.bodySite.coding",
                "path": "Specimen.collection.bodySite.coding",
                "slicing": {
                    "discriminator":  [
                        {
                            "type": "value",
                            "path": "system"
                        }
                    ],
                    "rules": "open"
                }
            },
            {
                "id": "Specimen.collection.bodySite.coding:snomedCT",
                "path": "Specimen.collection.bodySite.coding",
                "sliceName": "snomedCT",
                "max": "1",
                "binding": {
                    "strength": "preferred",
                    "description": "A code from the SNOMED UK Clinical Terminology coding system",
                    "valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-SpecimenBodySite"
                }
            },
            {
                "id": "Specimen.collection.bodySite.coding:snomedCT.system",
                "path": "Specimen.collection.bodySite.coding.system",
                "min": 1,
                "fixedUri": "http://snomed.info/sct"
            },
            {
                "id": "Specimen.collection.bodySite.coding:snomedCT.code",
                "path": "Specimen.collection.bodySite.coding.code",
                "min": 1
            },
            {
                "id": "Specimen.collection.bodySite.coding:snomedCT.display",
                "extension":  [
                    {
                        "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable",
                        "valueBoolean": true
                    }
                ],
                "path": "Specimen.collection.bodySite.coding.display",
                "min": 1
            },
            {
                "id": "Specimen.processing.additive.identifier.assigner",
                "path": "Specimen.processing.additive.identifier.assigner",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization"
                        ]
                    }
                ]
            },
            {
                "id": "Specimen.container.identifier.assigner",
                "path": "Specimen.container.identifier.assigner",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization"
                        ]
                    }
                ]
            },
            {
                "id": "Specimen.note.author[x]",
                "path": "Specimen.note.author[x]",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient",
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Practitioner",
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-RelatedPerson",
                            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization"
                        ]
                    },
                    {
                        "code": "string"
                    }
                ]
            }
        ]
    }
}

Examples

DBlood Specimen - An example to illustrate a blood specimen for a patient.
Example UKCore-Specimen-BloodSpecimen

Example Usage Scenarios

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

  • To be added during CTA 6

Bindings (differential)

More information about the bindings to UK Core ValueSets can be found below.

Context Strength Link
Specimen.type:snomedCT Preferred ValueSet UKCore-SpecimenType
Specimen.collection.bodySite:snomedCT Preferred ValueSet UKCore-SpecimenBodySite

type

This has been profiled using the slice Specimen.type:snomedCT.

If a SNOMED CT concept from the ValueSet UKCore-SpecimenType is used, and the concept is a descendant of "105590001 | Substance", Specimen.collection.method and Specimen.collection.bodySite SHOULD be populated.


subject

The resource being referenced SHOULD conform to one of the following:


parent

The resource being referenced SHOULD conform to the following Profile UKCore-Specimen.


request

The resource being referenced SHOULD conform to the following Profile UKCore-ServiceRequest.


collection

collection.collector

The resource being referenced SHOULD conform to one of the following:

collection.bodySite

This has been profiled using the slice Specimen.collection.bodySite:snomedCT.


note

The resource referenced in Specimen.note.authorReference SHOULD conform to one of the following:


back to top