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.

NamingSystem

Naming systems developed for use in Genomics. It is expected these will be proposed to HL7 UK for ratification at a UK level once development of the alpha build is underway.

NamingSystem

Genomic-Pedigree-Number

Clinical genetics no/pedigree number

HTML View

Kind

Identifier

Usage

Patient's genetic/pedigree number which links their family.

Unique IDs

type	Uri
value	https://fhir.nhs.uk/Id/genomics-pedigree-number
Preferred	True

Table View

NamingSystem.id[0]	genomics-pedigree-number
NamingSystem.name[0]	GenomicsPedigreeNumber
NamingSystem.status[0]	draft
NamingSystem.kind[0]	identifier
NamingSystem.date[0]	2022-12-05
NamingSystem.publisher[0]	NHS England
NamingSystem.contact[0].name[0]	NHS England
NamingSystem.contact[0].telecom[0].system[0]	email
NamingSystem.contact[0].telecom[0].value[0]	interoperabilityteam@nhs.net
NamingSystem.contact[0].telecom[0].use[0]	work
NamingSystem.contact[0].telecom[0].rank[0]	1
NamingSystem.contact[1].name[0]	NHS Genomic Medicine Service
NamingSystem.contact[1].telecom[0].system[0]	email
NamingSystem.contact[1].telecom[0].value[0]	england.genomics@nhs.net
NamingSystem.contact[1].telecom[0].use[0]	work
NamingSystem.contact[1].telecom[0].rank[0]	1
NamingSystem.responsible[0]	NHS Genomic Interop Programme
NamingSystem.description[0]	Clinical genetics no/pedigree number
NamingSystem.usage[0]	Patient's genetic/pedigree number which links their family.
NamingSystem.uniqueId[0].type[0]	uri
NamingSystem.uniqueId[0].value[0]	https://fhir.nhs.uk/Id/genomics-pedigree-number
NamingSystem.uniqueId[0].preferred[0]	True

XML View

<NamingSystem xmlns="http://hl7.org/fhir">
    <id value="genomics-pedigree-number" />
    <name value="GenomicsPedigreeNumber" />
    <status value="draft" />
    <kind value="identifier" />
    <date value="2022-12-05" />
    <publisher value="NHS England" />
    <contact>
        <name value="NHS England" />
        <telecom>
            <system value="email" />
            <value value="interoperabilityteam@nhs.net" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <contact>
        <name value="NHS Genomic Medicine Service" />
        <telecom>
            <system value="email" />
            <value value="england.genomics@nhs.net" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <responsible value="NHS Genomic Interop Programme" />
    <description value="Clinical genetics no/pedigree number" />
    <usage value="Patient&#39;s genetic/pedigree number which links their family." />
    <uniqueId>
        <type value="uri" />
        <value value="https://fhir.nhs.uk/Id/genomics-pedigree-number" />
        <preferred value="true" />
    </uniqueId>
</NamingSystem>

JSON View

{
    "resourceType": "NamingSystem",
    "id": "genomics-pedigree-number",
    "name": "GenomicsPedigreeNumber",
    "status": "draft",
    "kind": "identifier",
    "date": "2022-12-05",
    "publisher": "NHS England",
    "contact":  [
        {
            "name": "NHS England",
            "telecom":  [
                {
                    "system": "email",
                    "value": "interoperabilityteam@nhs.net",
                    "use": "work",
                    "rank": 1
                }
            ]
        },
        {
            "name": "NHS Genomic Medicine Service",
            "telecom":  [
                {
                    "system": "email",
                    "value": "england.genomics@nhs.net",
                    "use": "work",
                    "rank": 1
                }
            ]
        }
    ],
    "responsible": "NHS Genomic Interop Programme",
    "description": "Clinical genetics no/pedigree number",
    "usage": "Patient's genetic/pedigree number which links their family.",
    "uniqueId":  [
        {
            "type": "uri",
            "value": "https://fhir.nhs.uk/Id/genomics-pedigree-number",
            "preferred": true
        }
    ]
}

Genomic-Order-Number

Genomic Medicine Service Unique Order Number

HTML View

Kind

Identifier

Usage

Assigned by central GMS system on receipt of a test order

Unique IDs

type	Uri
value	https://fhir.nhs.uk/Id/GMSOrder
Preferred	True

Table View

NamingSystem.id[0]	genomics-order-number
NamingSystem.name[0]	GenomicsOrderNumber
NamingSystem.status[0]	draft
NamingSystem.kind[0]	identifier
NamingSystem.date[0]	2023-09-15
NamingSystem.publisher[0]	NHS England
NamingSystem.contact[0].name[0]	NHS England
NamingSystem.contact[0].telecom[0].system[0]	email
NamingSystem.contact[0].telecom[0].value[0]	interoperabilityteam@nhs.net
NamingSystem.contact[0].telecom[0].use[0]	work
NamingSystem.contact[0].telecom[0].rank[0]	1
NamingSystem.contact[1].name[0]	NHS Genomic Medicine Service
NamingSystem.contact[1].telecom[0].system[0]	email
NamingSystem.contact[1].telecom[0].value[0]	england.genomics@nhs.net
NamingSystem.contact[1].telecom[0].use[0]	work
NamingSystem.contact[1].telecom[0].rank[0]	1
NamingSystem.responsible[0]	NHS Genomic Interop Programme
NamingSystem.description[0]	Genomic Medicine Service Unique Order Number
NamingSystem.usage[0]	Assigned by central GMS system on receipt of a test order
NamingSystem.uniqueId[0].type[0]	uri
NamingSystem.uniqueId[0].value[0]	https://fhir.nhs.uk/Id/GMSOrder
NamingSystem.uniqueId[0].preferred[0]	True

XML View

<NamingSystem xmlns="http://hl7.org/fhir">
    <id value="genomics-order-number" />
    <name value="GenomicsOrderNumber" />
    <status value="draft" />
    <kind value="identifier" />
    <date value="2023-09-15" />
    <publisher value="NHS England" />
    <contact>
        <name value="NHS England" />
        <telecom>
            <system value="email" />
            <value value="interoperabilityteam@nhs.net" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <contact>
        <name value="NHS Genomic Medicine Service" />
        <telecom>
            <system value="email" />
            <value value="england.genomics@nhs.net" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <responsible value="NHS Genomic Interop Programme" />
    <description value="Genomic Medicine Service Unique Order Number" />
    <usage value="Assigned by central GMS system on receipt of a test order" />
    <uniqueId>
        <type value="uri" />
        <value value="https://fhir.nhs.uk/Id/GMSOrder" />
        <preferred value="true" />
    </uniqueId>
</NamingSystem>

JSON View

{
    "resourceType": "NamingSystem",
    "id": "genomics-order-number",
    "name": "GenomicsOrderNumber",
    "status": "draft",
    "kind": "identifier",
    "date": "2023-09-15",
    "publisher": "NHS England",
    "contact":  [
        {
            "name": "NHS England",
            "telecom":  [
                {
                    "system": "email",
                    "value": "interoperabilityteam@nhs.net",
                    "use": "work",
                    "rank": 1
                }
            ]
        },
        {
            "name": "NHS Genomic Medicine Service",
            "telecom":  [
                {
                    "system": "email",
                    "value": "england.genomics@nhs.net",
                    "use": "work",
                    "rank": 1
                }
            ]
        }
    ],
    "responsible": "NHS Genomic Interop Programme",
    "description": "Genomic Medicine Service Unique Order Number",
    "usage": "Assigned by central GMS system on receipt of a test order",
    "uniqueId":  [
        {
            "type": "uri",
            "value": "https://fhir.nhs.uk/Id/GMSOrder",
            "preferred": true
        }
    ]
}

England-GenomicTestDirectory

NamingSystem for NHS England Genomic Test Directory codes

HTML View

Kind

Codesystem

Usage

Used to define the system for Genomic Test Directory codes within ServiceRequest resources

Unique IDs

type	Uri
value	https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory
Preferred	True

Table View

NamingSystem.id[0]	England-GenomicTestDirectory
NamingSystem.name[0]	EnglandGenomicTestDirectory
NamingSystem.status[0]	draft
NamingSystem.kind[0]	codesystem
NamingSystem.date[0]	2023-12-04
NamingSystem.publisher[0]	NHS England
NamingSystem.contact[0].name[0]	NHS England
NamingSystem.contact[0].telecom[0].system[0]	email
NamingSystem.contact[0].telecom[0].value[0]	interoperabilityteam@nhs.net
NamingSystem.contact[0].telecom[0].use[0]	work
NamingSystem.contact[0].telecom[0].rank[0]	1
NamingSystem.contact[1].name[0]	NHS Genomic Medicine Service
NamingSystem.contact[1].telecom[0].system[0]	email
NamingSystem.contact[1].telecom[0].value[0]	england.genomics@nhs.net
NamingSystem.contact[1].telecom[0].use[0]	work
NamingSystem.contact[1].telecom[0].rank[0]	1
NamingSystem.responsible[0]	NHS Genomic Interop Programme
NamingSystem.description[0]	NamingSystem for Genomic Test Directory Codes
NamingSystem.usage[0]	Used to define the system for Genomic Test Directory codes within ServiceRequest resources
NamingSystem.uniqueId[0].type[0]	uri
NamingSystem.uniqueId[0].value[0]	https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory
NamingSystem.uniqueId[0].preferred[0]	True

XML View

<NamingSystem xmlns="http://hl7.org/fhir">
    <id value="England-GenomicTestDirectory" />
    <name value="EnglandGenomicTestDirectory" />
    <status value="draft" />
    <kind value="codesystem" />
    <date value="2023-12-04" />
    <publisher value="NHS England" />
    <contact>
        <name value="NHS England" />
        <telecom>
            <system value="email" />
            <value value="interoperabilityteam@nhs.net" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <contact>
        <name value="NHS Genomic Medicine Service" />
        <telecom>
            <system value="email" />
            <value value="england.genomics@nhs.net" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <responsible value="NHS Genomic Interop Programme" />
    <description value="NamingSystem for Genomic Test Directory Codes" />
    <usage value="Used to define the system for Genomic Test Directory codes within ServiceRequest resources" />
    <uniqueId>
        <type value="uri" />
        <value value="https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory" />
        <preferred value="true" />
    </uniqueId>
</NamingSystem>

JSON View

{
    "resourceType": "NamingSystem",
    "id": "England-GenomicTestDirectory",
    "name": "EnglandGenomicTestDirectory",
    "status": "draft",
    "kind": "codesystem",
    "date": "2023-12-04",
    "publisher": "NHS England",
    "contact":  [
        {
            "name": "NHS England",
            "telecom":  [
                {
                    "system": "email",
                    "value": "interoperabilityteam@nhs.net",
                    "use": "work",
                    "rank": 1
                }
            ]
        },
        {
            "name": "NHS Genomic Medicine Service",
            "telecom":  [
                {
                    "system": "email",
                    "value": "england.genomics@nhs.net",
                    "use": "work",
                    "rank": 1
                }
            ]
        }
    ],
    "responsible": "NHS Genomic Interop Programme",
    "description": "NamingSystem for Genomic Test Directory Codes",
    "usage": "Used to define the system for Genomic Test Directory codes within ServiceRequest resources",
    "uniqueId":  [
        {
            "type": "uri",
            "value": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory",
            "preferred": true
        }
    ]
}

England-GenomicTestPanelCode

NamingSystem for NHS England Genomic Test Panel codes

HTML View

Kind

Codesystem

Usage

Used to define the system for Genomic Test Panel codes within ServiceRequest resources

Unique IDs

type	Uri
value	https://fhir.nhs.uk/CodeSystem/England-GenomicTestPanelCode
Preferred	True

Table View

NamingSystem.id[0]	England-GenomicTestPanelCode
NamingSystem.name[0]	EnglandGenomicTestPanelCode
NamingSystem.status[0]	draft
NamingSystem.kind[0]	codesystem
NamingSystem.date[0]	2023-05-23
NamingSystem.publisher[0]	NHS England
NamingSystem.contact[0].name[0]	NHS England
NamingSystem.contact[0].telecom[0].system[0]	email
NamingSystem.contact[0].telecom[0].value[0]	interoperabilityteam@nhs.net
NamingSystem.contact[0].telecom[0].use[0]	work
NamingSystem.contact[0].telecom[0].rank[0]	1
NamingSystem.contact[1].name[0]	NHS Genomic Medicine Service
NamingSystem.contact[1].telecom[0].system[0]	email
NamingSystem.contact[1].telecom[0].value[0]	england.genomics@nhs.net
NamingSystem.contact[1].telecom[0].use[0]	work
NamingSystem.contact[1].telecom[0].rank[0]	1
NamingSystem.responsible[0]	NHS Genomic Interop Programme
NamingSystem.description[0]	NamingSystem for Genomic Test Panel Codes
NamingSystem.usage[0]	Used to define the system for Genomic Test Panel codes within ServiceRequest resources
NamingSystem.uniqueId[0].type[0]	uri
NamingSystem.uniqueId[0].value[0]	https://fhir.nhs.uk/CodeSystem/England-GenomicTestPanelCode
NamingSystem.uniqueId[0].preferred[0]	True

XML View

<NamingSystem xmlns="http://hl7.org/fhir">
    <id value="England-GenomicTestPanelCode" />
    <name value="EnglandGenomicTestPanelCode" />
    <status value="draft" />
    <kind value="codesystem" />
    <date value="2023-05-23" />
    <publisher value="NHS England" />
    <contact>
        <name value="NHS England" />
        <telecom>
            <system value="email" />
            <value value="interoperabilityteam@nhs.net" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <contact>
        <name value="NHS Genomic Medicine Service" />
        <telecom>
            <system value="email" />
            <value value="england.genomics@nhs.net" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <responsible value="NHS Genomic Interop Programme" />
    <description value="NamingSystem for Genomic Test Panel Codes" />
    <usage value="Used to define the system for Genomic Test Panel codes within ServiceRequest resources" />
    <uniqueId>
        <type value="uri" />
        <value value="https://fhir.nhs.uk/CodeSystem/England-GenomicTestPanelCode" />
        <preferred value="true" />
    </uniqueId>
</NamingSystem>

JSON View

{
    "resourceType": "NamingSystem",
    "id": "England-GenomicTestPanelCode",
    "name": "EnglandGenomicTestPanelCode",
    "status": "draft",
    "kind": "codesystem",
    "date": "2023-05-23",
    "publisher": "NHS England",
    "contact":  [
        {
            "name": "NHS England",
            "telecom":  [
                {
                    "system": "email",
                    "value": "interoperabilityteam@nhs.net",
                    "use": "work",
                    "rank": 1
                }
            ]
        },
        {
            "name": "NHS Genomic Medicine Service",
            "telecom":  [
                {
                    "system": "email",
                    "value": "england.genomics@nhs.net",
                    "use": "work",
                    "rank": 1
                }
            ]
        }
    ],
    "responsible": "NHS Genomic Interop Programme",
    "description": "NamingSystem for Genomic Test Panel Codes",
    "usage": "Used to define the system for Genomic Test Panel codes within ServiceRequest resources",
    "uniqueId":  [
        {
            "type": "uri",
            "value": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestPanelCode",
            "preferred": true
        }
    ]
}