FHIR Genomics Implementation Guide

Notice

Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.

Specimen-PatrickSammyBoneMarrowAspiration-Example

Example of a specimen resource with additional collection information on specimen condition and category.

Specimen

id : Specimen-PatrickSammyBoneMarrowAspiration-Example

extension

url : https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory

value

coding

system : https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory

code : liquid-tumour

display : Liquid Tumour

identifier

system : urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24

value : RR81235

assigner

identifier

system : https://fhir.nhs.uk/Id/ods-organization-code

value : 696B0

accessionIdentifier

system : https://www.leedsth.nhs.uk/path

value : RR8123745

assigner

identifier

system : https://fhir.nhs.uk/Id/ods-organization-code

value : RR8

status : available

type

coding

system : http://snomed.info/sct

code : 396997002

display : Specimen from bone marrow obtained by aspiration

subject

reference : Patient/Patient-PatrickSammy-Example

identifier

system : https://fhir.nhs.uk/Id/nhs-number

value : 9449307873

receivedTime : 2023-09-11T11:00:00Z

condition

coding

system : http://terminology.hl7.org/CodeSystem/v2-0493

code : FROZ

display : Frozen

request

reference : ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example

{
    "resourceType": "Specimen",
    "id": "Specimen-PatrickSammyBoneMarrowAspiration-Example",
    "extension":  [
        {
            "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory",
            "valueCodeableConcept": {
                "coding":  [
                    {
                        "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory",
                        "code": "liquid-tumour",
                        "display": "Liquid Tumour"
                    }
                ]
            }
        }
    ],
    "identifier":  [
        {
            "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24",
            "value": "RR81235",
            "assigner": {
                "identifier": {
                    "system": "https://fhir.nhs.uk/Id/ods-organization-code",
                    "value": "696B0"
                }
            }
        }
    ],
    "accessionIdentifier": {
        "system": "https://www.leedsth.nhs.uk/path",
        "value": "RR8123745",
        "assigner": {
            "identifier": {
                "system": "https://fhir.nhs.uk/Id/ods-organization-code",
                "value": "RR8"
            }
        }
    },
    "status": "available",
    "type": {
        "coding":  [
            {
                "system": "http://snomed.info/sct",
                "code": "396997002",
                "display": "Specimen from bone marrow obtained by aspiration"
            }
        ]
    },
    "subject": {
        "reference": "Patient/Patient-PatrickSammy-Example",
        "identifier": {
            "system": "https://fhir.nhs.uk/Id/nhs-number",
            "value": "9449307873"
        }
    },
    "receivedTime": "09/11/2023 11:00:00",
    "condition":  [
        {
            "coding":  [
                {
                    "system": "http://terminology.hl7.org/CodeSystem/v2-0493",
                    "code": "FROZ",
                    "display": "Frozen"
                }
            ]
        }
    ],
    "request":  [
        {
            "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example"
        }
    ]
}

<Specimen xmlns="http://hl7.org/fhir">
    <id value="Specimen-PatrickSammyBoneMarrowAspiration-Example" />
    <extension url="https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory">
        <valueCodeableConcept>
            <coding>
                <system value="https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory" />
                <code value="liquid-tumour" />
                <display value="Liquid Tumour" />
            </coding>
        </valueCodeableConcept>
    </extension>
    <identifier>
        <system value="urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24" />
        <value value="RR81235" />
        <assigner>
            <identifier>
                <system value="https://fhir.nhs.uk/Id/ods-organization-code" />
                <value value="696B0" />
            </identifier>
        </assigner>
    </identifier>
    <accessionIdentifier>
        <system value="https://www.leedsth.nhs.uk/path" />
        <value value="RR8123745" />
        <assigner>
            <identifier>
                <system value="https://fhir.nhs.uk/Id/ods-organization-code" />
                <value value="RR8" />
            </identifier>
        </assigner>
    </accessionIdentifier>
    <status value="available" />
    <type>
        <coding>
            <system value="http://snomed.info/sct" />
            <code value="396997002" />
            <display value="Specimen from bone marrow obtained by aspiration" />
        </coding>
    </type>
    <subject>
        <reference value="Patient/Patient-PatrickSammy-Example" />
        <identifier>
            <system value="https://fhir.nhs.uk/Id/nhs-number" />
            <value value="9449307873" />
        </identifier>
    </subject>
    <receivedTime value="2023-09-11T11:00:00Z" />
    <request>
        <reference value="ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example" />
    </request>
    <condition>
        <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0493" />
            <code value="FROZ" />
            <display value="Frozen" />
        </coding>
    </condition>
</Specimen>

Notice

Specimen-PatrickSammyBoneMarrowAspiration-Example

Propose a change to Specimen-PatrickSammyBoneMarrowAspiration-Example