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.

CapabilityStatements

Example CapabilityStatements to represent possible functionality of Genomics Services are listed below. These include Requirements, defining the profiles to be targeted during validation, and CapabilityStatements defining the endpoints for the Genomic Medicine Service. These services are currently in development, so the CapabilityStatment SHOULD NOT be taken as representations of implementations. Instead, the /metadata endpoint exposed by the specific service SHOULD be queried to identify the operations supported.

The API interactions that make up the service are a combination of FHIR transactions which allow multiple resources to be created and updated at once, and instance level interactions to retrieve or update specific FHIR resources.

The central Order Management Service will expose API endpoints to enable organisations to create and query test requests, tasks and linked FHIR Resources.

In the linked tables below the API interactions which can be used to create, update and search for information on the test ordering services are specified at a high level.

Note: The “Create ServiceRequest”, “Create Task” and “Create Specimen” are all FHIR resource level interactions and could all be performed within one transaction to reduce the number of API calls required, for example if a GLH creates a new specimen, which they are going to send to an LGL, they should POST the new Specimen, Task and all related resources in one request.

CapabilityStatements

Requirements

REST Capabilities Server

Mode	Server

Security

Service	OAuth2 Token

Resource Interactions

Resource Type	Profile	Supported Profiles
AuditEvent	NHSEngland_AuditEvent_GenomicsPARS
Bundle	NHSEngland_Bundle_Genomics
Composition	NHSEngland_Composition_GenomicsEULabReport
DocumentReference	NHSEngland_DocumentReference_GenomicDataFile
CodeSystem	CodeSystem
GraphDefinition	GraphDefinition
ConceptMap	ConceptMap
HealthcareService	UKCoreHealthcareService
MessageDefinition	MessageDefinition
NamingSystem	NamingSystem
Parameters	Parameters
StructureMap	StructureMap
ValueSet	ValueSet
MessageHeader	MessageHeader
Subscription	Subscription
CapabilityStatement	CapabilityStatement
Task	NHSEngland_Task_Genomics
ServiceRequest	NHSEngland_ServiceRequest_Genomics
PractitionerRole	NHSEngland_PractitionerRole_Genomics
Practitioner	UKCorePractitioner
Organization	UKCoreOrganization
DiagnosticReport	NHSEngland_DiagnosticReport_GenomicReport
FamilyMemberHistory	NHSEngland_FamilyMemberHistory_Genomics
Observation	NHSEngland_Observation_GenomicsLab
Patient	NHSEngland_Patient_Genomics
Consent	NHSEngland_Consent_GenomicsPCF
Condition	NHSEngland_Condition_GenomicsmCODE
ResearchSubject	ResearchSubject
RelatedPerson	NHSEngland_RelatedPerson_Genomics
Specimen	NHSEngland_Specimen_Genomics
Questionnaire	Questionnaire
QuestionnaireResponse	QuestionnaireResponse
OperationDefinition	OperationDefinition
OperationOutcome	OperationOutcome
BodyStructure	NHSEngland_BodyStructure_GenomicsmCODE
Provenance	NHSEngland_Provenance_Genomics
RequestGroup	NHSEngland_RequestGroup_Genomics

Instance

REST Capabilities Server

Mode	Server
Documentation	RESTful endpoints supported by the Genomic Medicine Service

Security

Service	OAuth2 Token

Resource Interactions

Resource Type	Profile	Read	SearchType	Create	Vread	Update	Patch	Delete	HistoryInstance	ConditionalCreate
AuditEvent	NHSEngland_AuditEvent_GenomicsPARS	✓	✓
Bundle	NHSEngland_Bundle_Genomics			✓						✓
CodeSystem	CodeSystem	✓	✓
GraphDefinition	GraphDefinition	✓	✓
ConceptMap	ConceptMap	✓	✓
HealthcareService	UKCoreHealthcareService	✓	✓	✓	✓	✓	✓	✓	✓	✓
MessageDefinition	MessageDefinition	✓	✓
NamingSystem	NamingSystem	✓	✓
Parameters	Parameters
StructureMap	StructureMap	✓	✓
ValueSet	ValueSet	✓	✓
MessageHeader	MessageHeader	✓	✓	✓						✓
Subscription	Subscription	✓	✓	✓	✓	✓	✓	✓	✓	✓
CapabilityStatement	CapabilityStatement	✓	✓
Task	NHSEngland_Task_Genomics	✓	✓	✓	✓	✓	✓	✓	✓	✓
ServiceRequest	NHSEngland_ServiceRequest_Genomics	✓	✓	✓	✓	✓	✓	✓	✓	✓
PractitionerRole	NHSEngland_PractitionerRole_Genomics	✓	✓	✓	✓	✓	✓	✓	✓	✓
Practitioner	UKCorePractitioner	✓	✓	✓	✓	✓	✓	✓	✓	✓
Organization	UKCoreOrganization	✓	✓	✓	✓	✓	✓	✓	✓	✓
DiagnosticReport	NHSEngland_DiagnosticReport_GenomicReport	✓	✓	✓	✓	✓	✓	✓	✓	✓
FamilyMemberHistory	NHSEngland_FamilyMemberHistory_Genomics	✓	✓	✓	✓	✓	✓	✓	✓	✓
Observation	NHSEngland_Observation_GenomicsLab	✓	✓	✓	✓	✓	✓	✓	✓	✓
Patient	NHSEngland_Patient_Genomics	✓	✓	✓	✓	✓	✓	✓	✓	✓
Consent	NHSEngland_Consent_GenomicsPCF	✓	✓	✓	✓	✓	✓	✓	✓	✓
Condition	NHSEngland_Condition_GenomicsmCODE	✓	✓	✓	✓	✓	✓	✓	✓	✓
ResearchSubject	ResearchSubject
RelatedPerson	NHSEngland_RelatedPerson_Genomics	✓	✓	✓	✓	✓	✓	✓	✓	✓
Specimen	NHSEngland_Specimen_Genomics	✓	✓	✓	✓	✓	✓	✓	✓	✓
Questionnaire	Questionnaire	✓	✓
QuestionnaireResponse	QuestionnaireResponse	✓	✓	✓	✓	✓	✓	✓	✓	✓
OperationDefinition	OperationDefinition
OperationOutcome	OperationOutcome	✓	✓
BodyStructure	NHSEngland_BodyStructure_GenomicsmCODE	✓	✓	✓	✓	✓	✓	✓	✓	✓
Provenance	NHSEngland_Provenance_Genomics	✓	✓
DocumentReference	NHSEngland_DocumentReference_GenomicDataFile	✓	✓	✓	✓	✓	✓	✓	✓	✓
Composition	NHSEngland_Composition_GenomicsEULabReport		✓
RequestGroup	NHSEngland_RequestGroup_Genomics	✓	✓

Search Parameters per resource type

AuditEvent

Name	Type	Level
action	token	Supported
agent	reference	Supported
date	date	Supported
entity	reference	Supported
outcome	token	Supported
patient	reference	Supported

Bundle

No search parameters are stated for this resource type

CodeSystem

Name	Type	Level
code	token	Supported
context	token	Supported
description	string	Supported
identifier	token	Supported
name	string	Supported
system	uri	Supported
title	string	Supported

GraphDefinition

Name	Type	Level
name	string	Supported
start	token	Supported

ConceptMap

Name	Type	Level
context	token	Supported
description	string	Supported
identifier	token	Supported
name	string	Supported
source-system	uri	Supported
target-system	uri	Supported
title	string	Supported

HealthcareService

Name	Type	Level
coverage-area	reference	Supported
endpoint	reference	Supported
identifier	token	Supported
name	string	Supported
location	reference	Supported
organization	reference	Supported
service-category	token	Supported
service-type	token	Supported
specialty	token	Supported

MessageDefinition

Name	Type	Level
description	string	Supported
identifier	token	Supported
name	string	Supported
focus	token	Supported
title	string	Supported

NamingSystem

Name	Type	Level
context	token	Supported
description	string	Supported
name	string	Supported

Parameters

No search parameters are stated for this resource type

StructureMap

Name	Type	Level
context	token	Supported
description	string	Supported
identifier	token	Supported
name	string	Supported

ValueSet

Name	Type	Level
code	token	Supported
context	token	Supported
description	string	Supported
identifier	token	Supported
name	string	Supported
title	string	Supported

MessageHeader

Name	Type	Level
code	token	Supported
destination	string	Supported
destination-uri	uri	Supported
focus	reference	Supported
sender	reference	Supported
source	string	Supported
source-uri	uri	Supported

Subscription

Name	Type	Level
contact	token	Supported
criteria	string	Supported
status	token	Supported
type	token	Supported
url	uri	Supported

CapabilityStatement

Name	Type	Level
description	string	Supported
format	token	Supported
mode	token	Supported
name	string	Supported
resource	token	Supported
resource-profile	reference	Supported
title	string	Supported

Task

Name	Type	Level
based-on	reference	Supported
business-status	token	Supported
code	token	Supported
focus	reference	Supported
modified	date	Supported
owner	reference	Supported
subject	reference	Supported
performer	token	Supported
period	date	Supported
priority	token	Supported
requester	reference	Supported
status	token	Supported

ServiceRequest

Name	Type	Level
authored	date	Supported
based-on	reference	Supported
category	token	Supported
code	token	Supported
identifier	token	Supported
intent	token	Supported
subject	reference	Supported
performer	reference	Supported
performer-type	token	Supported
priority	token	Supported
replaces	reference	Supported
requester	reference	Supported
requisition	token	Supported
specimen	reference	Supported
status	token	Supported
supporting-info	reference	Supported

PractitionerRole

Name	Type	Level
endpoint	reference	Supported
identifier	token	Supported
organization	reference	Supported
practitioner	reference	Supported
specialty	token	Supported
telecom	token	Supported

Practitioner

Name	Type	Level
name	string	Supported
identifier	token	Supported

Organization

Name	Type	Level
address	string	Supported
endpoint	reference	Supported
identifier	token	Supported
name	string	Supported
partof	reference	Supported
type	token	Supported

DiagnosticReport

Name	Type	Level
based-on	reference	Supported
category	token	Supported
code	token	Supported
conclusion	token	Supported
date	date	Supported
identifier	token	Supported
issued	date	Supported
subject	reference	Supported
performer	reference	Supported
result	reference	Supported
results-interpreter	reference	Supported
specimen	reference	Supported
status	token	Supported

FamilyMemberHistory

Name	Type	Level
code	token	Supported
date	date	Supported
identifier	token	Supported
patient	reference	Supported
relationship	token	Supported
sex	token	Supported
status	token	Supported

Observation

Name	Type	Level
based-on	reference	Supported
category	token	Supported
code	token	Supported
component-code	token	Supported
data-absent-reason	token	Supported
date	date	Supported
focus	reference	Supported
identifier	token	Supported
subject	reference	Supported
performer	reference	Supported
specimen	reference	Supported
value-string	string	Supported
status	token	Supported

Patient

Name	Type	Level
address	string	Supported
birthdate	date	Supported
death-date	token	Supported
gender	token	Supported
general-practitioner	reference	Supported
identifier	token	Supported
link	reference	Supported
name	string	Supported
organization	reference	Supported
telecom	token	Supported

Consent

Name	Type	Level
action	token	Supported
actor	reference	Supported
category	token	Supported
consentor	reference	Supported
identifier	token	Supported
organization	reference	Supported
patient	reference	Supported
period	date	Supported

Condition

Name	Type	Level
asserter	reference	Supported
category	token	Supported
clinical-status	token	Supported
code	token	Supported
identifier	token	Supported
onset-info	string	Supported
subject	reference	Supported
recorded-date	date	Supported
severity	token	Supported
stage	token	Supported
verification-status	token	Supported

ResearchSubject

No search parameters are stated for this resource type

RelatedPerson

Name	Type	Level
patient	reference	Supported
relationship	token	Supported

Specimen

Name	Type	Level
accession	token	Supported
bodysite	token	Supported
collected	date	Supported
collector	reference	Supported
container-id	token	Supported
identifier	token	Supported
parent	reference	Supported
subject	reference	Supported
status	token	Supported
type	token	Supported
request	reference	Supported

Questionnaire

Name	Type	Level
date	date	Supported
description	string	Supported
effective	date	Supported
identifier	token	Supported
name	string	Supported
status	token	Supported
title	string	Supported
version	token	Supported

QuestionnaireResponse

Name	Type	Level
author	reference	Supported
authored	date	Supported
identifier	token	Supported
subject	reference	Supported
questionnaire	reference	Supported
source	reference	Supported
status	token	Supported

OperationDefinition

No search parameters are stated for this resource type

OperationOutcome

No search parameters are stated for this resource type

BodyStructure

Name	Type	Level
identifier	token	Supported
location	token	Supported
morphology	token	Supported
patient	reference	Supported

Provenance

Name	Type	Level
agent	reference	Supported
entity	reference	Supported
target	reference	Supported
recorded	date	Supported

DocumentReference

Name	Type	Level
date	date	Supported
subject	reference	Supported

Composition

Name	Type	Level
type	token	Supported
subject	reference	Supported
entry	reference	Supported
date	date	Supported

RequestGroup

Name	Type	Level
identifier	token	Supported
patient	reference	Supported
status	token	Supported
authorOn	date	Supported
intent	token	Supported

Messaging Capabilities

Endpoints

Protocol	Address
HTTP	https://[baseUrl]/$process-message

Documentation

Endpoint which accepts test order and result message bundles. The server saves the whole message as well as splitting the message into its individual resources for ease of updating through RESTful interactions

Supported Messages

Mode	Definition
Receiver	GenomicTestRequest
Receiver	GenomicTestResponse

DGTS

REST Capabilities Server

Mode	Server
Documentation	RESTful endpoints supported by the DGTS FHIR API

Resource Interactions

Resource Type	Profile	Read	SearchType
PlanDefinition	PlanDefinition	✓	✓
ActivityDefinition	ActivityDefinition	✓	✓
Library	Library	✓
SpecimenDefinition	SpecimenDefinition	✓

Operations per resource type

PlanDefinition

No operations are stated for this resource type

ActivityDefinition

Operation	Reference	Level
$data-requirements	Data Requirements	Supported

Library

No operations are stated for this resource type

SpecimenDefinition

No operations are stated for this resource type

Search Parameters per resource type

PlanDefinition

Name	Type	Documentation	Level
context	token		Supported
identifier	token		Supported
status	token		Supported
title	string		Supported
url	uri		Supported
version	token		Supported
actor-role	token	Search PlanDefinition by actor option role from the R5 cross-version extension extension-PlanDefinition.actor	Supported
actor-type-reference	reference	Search PlanDefinition by actor option typeReference from the R5 cross-version extension extension-PlanDefinition.actor	Supported

ActivityDefinition

Name	Type	Level
composed-of	reference	Supported
context	token	Supported
identifier	token	Supported
title	string	Supported
status	token	Supported
url	uri	Supported
version	token	Supported

Library

No search parameters are stated for this resource type

SpecimenDefinition

No search parameters are stated for this resource type

UGR

REST Capabilities Server

Mode	Server
Documentation	RESTful endpoints supported by the UGR FHIR API

Resource Interactions

Resource Type	Profile	Read	SearchType	Vread	HistoryInstance	Update	Patch	Delete	Create	ConditionalCreate
Composition	NHSEngland_Composition_GenomicsEULabReport	✓	✓	✓	✓
RelatedPerson	NHSEngland_RelatedPerson_Genomics	✓	✓	✓	✓	✓	✓	✓	✓	✓
Consent	NHSEngland_Consent_GenomicsPCF	✓	✓	✓	✓	✓	✓	✓	✓	✓

Operations per resource type

Composition

Operation	Reference	Level
$document	Generate a Document	Supported

RelatedPerson

No operations are stated for this resource type

Consent

No operations are stated for this resource type

Search Parameters per resource type

Composition

Name	Type	Level
type	token	Supported
subject	reference	Supported
entry	reference	Supported
date	date	Supported

RelatedPerson

Name	Type	Level
active	token	Supported
identifier	token	Supported
patient	reference	Supported
relationship	token	Supported

Consent

Name	Type	Level
action	token	Supported
actor	reference	Supported
category	token	Supported
consentor	reference	Supported
data	reference	Supported
patient	reference	Supported
period	date	Supported
purpose	token	Supported
scope	token	Supported
status	token	Supported