diff --git a/specification/beta/genomic-order-management-service-api-specification-beta.yaml b/specification/beta/genomic-order-management-service-api-specification-beta.yaml index 83361aa..f4e0f71 100644 --- a/specification/beta/genomic-order-management-service-api-specification-beta.yaml +++ b/specification/beta/genomic-order-management-service-api-specification-beta.yaml @@ -1,7 +1,7 @@ openapi: 3.0.3 info: title: Genomic Order Management Service (FHIR) API - version: v0.5.2 Beta + version: v0.5.3 Beta description: > ## Overview @@ -140,11 +140,11 @@ info: (RBAC)](https://digital.nhs.uk/developer/guides-and-documentation/security-and-authorisation/national-rbac-for-developers) - RBAC rules are stored in the National RBAC Database (NRD) and are used to limit what clinical users can and cannot do. - + * [Digital Genomics Test Directory Service (DGTS)](https://digital.nhs.uk/developer/api-catalogue/digital-genomics-test-directory-service) - Search for Genomic Tests and Test Packages using FHIR - + * [Multicast Notification Service (MNS)](https://digital.nhs.uk/developer/api-catalogue/multicast-notification-service) - Notification service for genomic events @@ -352,7 +352,7 @@ info: | Integration |`https://int.api.service.nhs.uk/genomic-order-management-service`| - + | Production |`https://api.service.nhs.uk/genomic-order-management-service`| @@ -469,7 +469,7 @@ paths: description: | ## Overview [FHIR Restful](https://hl7.org/fhir/R4/http.html) endpoint to - register a **new test or update tests or add reports etc**. This end point uses FHIR [bundle](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Bundle) of type **transaction** and the list of resources that forms the payload are listed [here](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/Build/Resource-Linkage). + register a **new test or update tests or add reports etc**. This end point uses FHIR [bundle](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Bundle) of type **transaction** and the list of resources that forms the payload are listed [here](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/Build/Resource-Linkage). tags: - process parameters: @@ -1919,7 +1919,7 @@ paths: This endpoint allows you to retrieve the records of DiagnosticReport using various query parameters. Refer [search](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/Build/Supported-CRUD-capability#Read) for more details. - + ## UGR - Search for patient test reports. tags: - report @@ -2133,7 +2133,7 @@ paths: | Scenario | - Request + Request | Response | @@ -2143,8 +2143,8 @@ paths: ------------------------------------------------------------------------| | - | - | + | + | | tags: - history @@ -2177,7 +2177,7 @@ paths: | Scenario | - Request + Request | Response | @@ -2187,7 +2187,7 @@ paths: ------------------------------------------------------------------------| | - | + | | | tags: @@ -3533,7 +3533,7 @@ components: - type - entry description: >- - A Bundle containing [FHIR ServiceRequest](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-ServiceRequest) + A Bundle containing [FHIR ServiceRequest](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-ServiceRequest) history examples: multiple-items: diff --git a/specification/enviroment/beta/genomic-order-management-service-api-specification-beta-dev.yaml b/specification/enviroment/beta/genomic-order-management-service-api-specification-beta-dev.yaml new file mode 100644 index 0000000..c8b6b03 --- /dev/null +++ b/specification/enviroment/beta/genomic-order-management-service-api-specification-beta-dev.yaml @@ -0,0 +1,4797 @@ +openapi: 3.0.3 +info: + title: Genomic Order Management Service (FHIR) API + version: v0.5.3 Beta + description: > + + ## Overview + + The [NHS Genomic Medicine Service](https://www.england.nhs.uk/genomics/) + enables the NHS to harness the power of genomic technology and science to + improve the health of our population and deliver on the commitments in the + [NHS Long Term Plan](https://www.longtermplan.nhs.uk/) including: + + * to be the first national health care system to offer whole genome + sequencing as part of routine care, including for all children with cancer + or children who are seriously ill with a likely genetic disorder + + * increased access to molecular diagnostics and offer genomic testing + routinely to all people with cancer + + * improve early detection and treatment of high-risk conditions including + expanding genomic testing for familial hypocholesterolaemia + + * linking and correlating genomic data to help provide new treatments, + diagnostic approaches and help patients make informed decisions about their + care + + + A + [strategy](https://www.england.nhs.uk/long-read/accelerating-genomic-medicine-in-the-nhs/) + for embedding genomics in the NHS over the next 5 years was published in + October 2022 outlined four priority areas: + + 1. embedding genomics across the NHS, through a world leading innovative + service model from primary and community care through to specialist and + tertiary care + + + 2. delivering equitable genomic testing for improved outcomes in cancer, + rare, inherited and common diseases and in enabling precision medicine and + reducing adverse drug reactions + + + 3. enabling genomics to be at the forefront of the data and digital + revolution, ensuring genomic data can be interpreted and informed by other + diagnostic and clinical data + + + 4. evolving the service through cutting-edge science, research and + innovation to ensure that patients can benefit from rapid implementation of + advances + + + + The Genomic Order Management service forms part of the core digital service + in enabling to accelerate services into clinical settings. The scope of this + service is the digitisation of **genomics test ordering and reporting** + within the whole of NHSE, focusing solely on test order management (Whole + Genome Sequencing (WGS) and Non-WGS Test Requests) and the management of + test results and reports. Key points in scope: + + * it is a central national capability, which will standardise the data + associated with each genomic test request and communication standards + + * it is focusing on the relevant data flows between organisational + boundaries + + + * with the end strategic goal being that a significant proportion of + requesting locations have their systems (e.g., EHRs, Portals, LIMS, Order + Comms) and receiving locations (e.g., Lab LIMS) integrated to central + national capability + + + Clinical users in NHS will be able to: + + * create requests for genomics tests + + + * track status updates to tests + + + * retrieve interpretation reports + + + Users in NHS Genomics Laboratories will be able to: + + * access genomic tests + + + * manage send aways + + + * update genomic tests + + + * create, Manage and Reassign tasks + + + * provide status updates on test progress + + + * upload interpretation reports + + + + The API's provide the core capabilities around the patient Unified Genomic + Record (**UGR**). + + + ## Who can use this API + This API can only be used where there is a legal basis to do so. Make sure you have a valid use case before you go too far with your development. + + ## Related APIs + + ### Services + + These services must be used alongside genomic order management service to + create a genetic test request, status tracking, updates and report access: + + * [Care Identity Service + 2](https://digital.nhs.uk/services/identity-and-access-management/national-care-identity-service) + [(CIS2)](https://digital.nhs.uk/services/care-identity-service/applications-and-services#cis2-authentication) + - use this to authenticate clinical users with their smartcard. See Security + and Authorisation + [section](https://digital.nhs.uk/developer/api-catalogue/genomic-order-management-service-fhir#overview--security-and-authorisation) + for more details. + + * [Organisation Data Service + (ODS)](https://digital.nhs.uk/developer/api-catalogue/organisation-data-service-fhir) + - use this to access ODS codes for NHS organisations using the genomics + services. + + * [Personal Demographics Service + (PDS)](https://digital.nhs.uk/developer/api-catalogue/personal-demographics-service-fhir) + - use PDS to synchronise a patient's demographic details including their + name, date of birth and address. + + * [Role-Based Access Controls + (RBAC)](https://digital.nhs.uk/developer/guides-and-documentation/security-and-authorisation/national-rbac-for-developers) + - RBAC rules are stored in the National RBAC Database (NRD) and are used to + limit what clinical users can and cannot do. + + * [Digital Genomics Test Directory Service + (DGTS)](https://digital.nhs.uk/developer/api-catalogue/digital-genomics-test-directory-service) + - Search for Genomic Tests and Test Packages using FHIR + + * [Multicast Notification Service + (MNS)](https://digital.nhs.uk/developer/api-catalogue/multicast-notification-service) + - Notification service for genomic events + + + ### Documentation + + This documentation provides important context: + + * [Genomic Test + Diretory](https://www.england.nhs.uk/publication/national-genomic-test-directories/) + - The national genomic test directory specifies which genomic tests are + commissioned by the NHS in England, the technology by which they are + available, and the patients who will be eligible to access to a test. + + * [Genomic Laboratory + Hubs](https://www.england.nhs.uk/genomics/genomic-laboratory-hubs/) - + Genomic testing in the NHS is being provided through a national testing + network, consolidating and enhancing the existing laboratory provision. + + + ### Guidance for developers and product owners + + Documentation and guidance for technical audiences: + + * [Implementation guide for Genomics FHIR + standard](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/Design/Interactions) + - the implementation guide contains detailed information, example, error + codes and processes. This is for technical audiences like developers. + + + * [FHIR UK Core R4](https://simplifier.net/hl7fhirukcorer4) - Core FHIR + standard mandated for adoption and implementation in UK and our [Genomics + IG]((https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/Design/Interactions) + is based on this standard. + + + ## API status and roadmap + + The data and digital framework established as part of the [genomics + strategy](https://www.england.nhs.uk/long-read/accelerating-genomic-medicine-in-the-nhs/) + outlined 3 major deliverables to accelerate the digital adoption and improve + services. + + * genomic order management service + + + * digital test directory + + + * unified genomic record + + + The immediate priority of Genomics Order Management development is to + support the rollout of the next-gen FHIR APIs for primary care and secondary + care settings for genetics ordering and GLH's in provding the testing + services. + + + This API is [in + development](https://digital.nhs.uk/developer/guides-and-documentation/reference-guide#statuses), + meaning: + + * it is available for testing in the integration environment + + + * we expect to make breaking changes based on developer feedback + + + + + ## Service level + + This API is a gold service, meaning it is operational and supported 24 + hours a day, 365 days a year. + + + For more details, see [service + levels](https://digital.nhs.uk/developer/guides-and-documentation/reference-guide#service-levels). + + + ## Technology + + This API is + [RESTful](https://digital.nhs.uk/developer/guides-and-documentation/our-api-technologies#basic-rest). + + + It conforms to the + [FHIR](https://digital.nhs.uk/developer/guides-and-documentation/our-api-technologies#fhir) + global standard for health care data exchange, specifically to [FHIR R4 + (v4.0.1)](https://hl7.org/fhir/r4/), except that it does not support the + [capabilities](http://hl7.org/fhir/R4/http.html#capabilities) interaction. + + Refer to [Genomics FHIR + IG](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home) + for more details to the implementation requirements. This specification is + based on UK Core Ballot2 and conforms to the same. + + + You do not need to know much about FHIR to use this API - FHIR APIs are just + RESTful APIs that follow specific rules. In particular: + + * resource names are capitalised and singular, for example `/Patient` not + `/patients` + + * array names are singular, for example `line` not `lines` for address lines + + * data items that are country-specific and thus not included in the FHIR + global base resources are usually wrapped in an `extension` object + + + There are [libraries and software development kits + available](https://digital.nhs.uk/developer/guides-and-documentation/api-technologies-at-nhs-digital#fhir-libraries-and-sdks) + to help with FHIR API integration. + + + ## Network access + + This API is available on the internet and, indirectly, on the [Health and + Social Care Network + (HSCN)](https://digital.nhs.uk/services/health-and-social-care-network). + + To use this API with [NHS + smartcards](https://digital.nhs.uk/developer/guides-and-documentation/security-and-authorisation/nhs-smartcards-for-developers), + the end user needs an HSCN connection, although internet-facing alternatives + to smartcards are available. + + + For more details see [Network access for + APIs](https://digital.nhs.uk/developer/guides-and-documentation/network-access-for-apis). + + + ## Security and authorisation + + This API has 2 access modes: + + * user-restricted access + + * application-restricted access + + + ### User-restricted access + + In LIVE the APIs are mostly + [user-restricted](https://digital.nhs.uk/developer/guides-and-documentation/security-and-authorisation#user-restricted-apis), + meaning we authenticate the end user. + + Our API's only supports [CIS2 separate authentication and + authorisation](https://digital.nhs.uk/developer/guides-and-documentation/security-and-authorisation/user-restricted-restful-apis-nhs-cis2-separate-authentication-and-authorisation),do + not use combined authentication and authorisation. + + ### Application-restricted access + + Use this access mode to communicate in unattended mode using application to application restricted mode. + + To use this access mode, use the following security pattern: + + * [Application-restricted RESTful API - signed JWT + authentication](https://digital.nhs.uk/developer/guides-and-documentation/security-and-authorisation/application-restricted-restful-apis-signed-jwt-authentication) + + + + **FOR PRIVATE BETA / LIVE** phase the API prefers consumers to implement [user-restricted + access](https://digital.nhs.uk/developer/guides-and-documentation/security-and-authorisation#user-restricted-apis) + based on + [CIS2](https://digital.nhs.uk/services/care-identity-service/applications-and-services#cis2-authentication) + for end user authentication. + + ## Errors + + We use standard HTTP status codes to show whether an API request succeeded + or not. They are usually in the range: + + + * 200 to 299 if it succeeded, including code 202 if it was accepted by an + API that needs to wait for further action + + + * 400 to 499 if it failed because of a client error by your application + + + * 500 to 599 if it failed because of an error on our server + + + Errors specific to each API are shown in the Endpoints section, under + Response. See our [reference + guide](https://digital.nhs.uk/developer/guides-and-documentation/reference-guide#http-status-codes) + for more on errors. + + ## Open source + + You might find the following [open + source](https://digital.nhs.uk/developer/guides-and-documentation/reference-guide#open-source) + resources useful. + + ## Environment and testing + + | Environment | Base + URL | + + |------------------|---------------------------------------------------------------------| + + | Sandbox (N/A) + |`https://sandbox.api.service.nhs.uk/genomic-order-management-service`| + + | Integration + |`https://int.api.service.nhs.uk/genomic-order-management-service`| + + | Production + |`https://api.service.nhs.uk/genomic-order-management-service`| + + ![Postman](https://run.pstmn.io/button.svg) collection to test against [INT environment](https://github.com/NHSDigital/genomic-order-management-service-api/tree/main/tests). + + ### Sandbox testing + + Our [sandbox + environment](https://digital.nhs.uk/developer/guides-and-documentation/testing#sandbox-testing): + + + * is for early developer testing + + * only covers a limited set of scenarios + + * is stateless, so it does not actually persist any updates + + * is open access, so does not allow you to test authorisation + + + For details of sandbox testing, or to try out the sandbox using our "Try + this API" feature, see the documentation for each endpoint. + + + ### Integration testing + + Our [integration test + environment](https://digital.nhs.uk/developer/guides-and-documentation/testing#integration-testing): + + + * is for formal integration testing + + * is stateful, so persists updates + + * includes authorisation, with + [smartcard](https://digital.nhs.uk/developer/guides-and-documentation/security-and-authorisation/nhs-smartcards-for-developers) + and non-smartcard options + + + For more details see [integration testing with our RESTful + APIs](https://digital.nhs.uk/developer/guides-and-documentation/testing#integration-testing-with-our-restful-apis). + + + ## Onboarding + + You need to get your software approved by us before it can go live with this + API. We call this onboarding. The onboarding process can sometimes be quite + long, so it is worth planning well ahead. + + + Whilst this API is in Alpha it is not possible to onboard to this API. As + part of this process, you need to demonstrate that you can manage risks and + that your software conforms technically with the requirements for this API. + Information on this page might impact the design of your software. + + + To understand how our online digital onboarding process works, see [digital + onboarding](https://digital.nhs.uk/developer/guides-and-documentation/digital-onboarding#using-the-digital-onboarding-portal). + + ## Contact us + + For help and support connecting to our APIs and to join our developer community, see [Help and support building healthcare software](https://digital.nhs.uk/developer/help-and-support). + +x-spec-publication: + operation-order: + - operations: + - method: POST + path: /FHIR/R4 + - operations: + - method: GET + path: /FHIR/R4/ServiceRequest + - operations: + - method: POST + path: /FHIR/R4/RequestGroup + - operations: + - method: GET + path: /FHIR/R4/Task + - operations: + - method: GET + path: /FHIR/R4/DiagnosticReport + - operations: + - method: POST + path: /FHIR/R4/Specimen + - operations: + - method: GET + path: /FHIR/R4/Specimen + - operations: + - method: GET + path: /FHIR/R4/Patient + - operations: + - method: GET + path: /FHIR/R4/PractitionerRole +servers: + - url: https://dev.api.service.nhs.uk/genomic-order-management-service + description: Development + - url: https://int.api.service.nhs.uk/genomic-order-management-service + description: Integration test + - url: https://api.service.nhs.uk/genomic-order-management-service + description: Production +tags: + - name: process + - name: order + - name: task + - name: report + - name: specimen + - name: patient + - name: practitionerrole + - name: relatedperson + - name: history + - name: meta +paths: + /FHIR/R4: + post: + operationId: processgenomicrequests + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Process genomic test request + description: | + ## Overview + [FHIR Restful](https://hl7.org/fhir/R4/http.html) endpoint to + register a **new test or update tests or add reports etc**. This end point uses FHIR [bundle](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Bundle) of type **transaction** and the list of resources that forms the payload are listed [here](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/Build/Resource-Linkage). + tags: + - process + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + requestBody: + required: true + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: > + A FHIR + [bundle](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Bundle) + with collection of [genomics test order request + resources.](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/MessageDefinitions/Genomic-Test-Request). + examples: + Non-WGS-Test-Request-Rare-Disease: + summary: Bundle-NonWGSTestOrderForm-Example + description: >- + Example + [transaction](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/Examples/Bundle/Bundle-NonWGSTestOrderForm-Example) + of a Non-WGS test request sent to the central broker, as + described in the Clinica Scenario [**Non-WGS Test Request - + Rare + Disease**](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/Design/Clinical-Scenarios#Non-WGS-Test-Request---Rare-Disease). + value: + resourceType: Bundle + id: Bundle-NonWGSTestOrderForm-Example + type: transaction + entry: + - fullUrl: >- + http://example.org/fhir/PractitionerRole/PractitionerRole-GeneSmithENT-Example + resource: + resourceType: PractitionerRole + id: PractitionerRole-GeneSmithENT-Example + practitioner: + identifier: + system: https://fhir.nhs.uk/Id/sds-user-id + value: '9999999999' + display: Dr. Gene Smith + organization: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RGT01 + display: Addenbrooke's Hospital + specialty: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-PracticeSettingCode + code: '120' + display: Ear Nose and Throat + telecom: + - system: phone + value: '01223586638' + - system: email + value: gene.smith@nhs.net + - system: email + value: Add-tr.entsecretaries@nhs.net + extension: + - url: >- + http://hl7.org/fhir/StructureDefinition/contactpoint-comment + valueString: reporting + request: + method: POST + url: PractitionerRole + - fullUrl: >- + http://example.org/fhir/Patient/Patient-MeirLieberman-Example + resource: + resourceType: Patient + id: Patient-MeirLieberman-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BirthSex + valueCodeableConcept: + coding: + - system: >- + http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender + code: M + display: Male + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-EthnicCategory + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-EthnicCategoryEngland + code: A + display: White - British + identifier: + - system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-NHSNumberVerificationStatus + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-NHSNumberVerificationStatusEngland + version: 2.2.0 + code: '01' + display: Number present and verified + - system: urn:oid:2.XX.XXX.X.XXXXXX.X.X.X.X.X.18.24 + value: RGT012423 + assigner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RGT01 + - system: https://fhir.nhs.uk/Id/genomics-pedigree-number + value: P12345 + name: + - given: + - Meir + - Anah + family: Lieberman + gender: male + birthDate: '2005-12-19' + deceasedBoolean: false + address: + - line: + - 1 Spinney Close + - Worcester Park + city: Surrey + postalCode: KT4 7BS + generalPractitioner: + - identifier: + system: https://fhir.hl7.org.uk/Id/gmp-number + value: G9999999 + display: Dr. Aero Smith + - identifier: + system: https://fhir.hl7.org.uk/Id/ODS-code + value: TP123 + display: 123 Test Practice + link: + - other: + reference: >- + https://api.service.nhs.uk/personal-demographics/FHIR/R4/Patient/9449307873 + type: seealso + request: + method: POST + url: Patient + ifNoneExist: >- + Patient?identifier=https://fhir.nhs.uk/Id/nhs-number|9449307873 + - fullUrl: >- + http://example.org/fhir/Observation/Observation-GenomicEthnicity-Example + resource: + resourceType: Observation + id: Observation-GenomicEthnicity-Example + status: preliminary + code: + coding: + - system: http://snomed.info/sct + code: '723621000000103' + display: Ethnicity + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + valueString: unknown + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/ServiceRequest/ServiceRequest-NonWGSTestOrderForm-Example + resource: + resourceType: ServiceRequest + id: ServiceRequest-NonWGSTestOrderForm-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory + code: nhs + display: NHS + status: active + intent: order + category: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory + code: rare-disease-non-wgs + display: Rare Disease - Non-WGS + priority: routine + code: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R67.2 + display: Monogenic hearing loss + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + authoredOn: '2023-08-05' + requester: + reference: >- + PractitionerRole/PractitionerRole-GeneSmithENT-Example + reasonCode: + - coding: + - system: http://snomed.info/sct + code: '103693007' + display: Diagnostic procedure + supportingInfo: + - reference: Observation/Observation-DiseaseStatus-Example + - reference: Observation/Observation-GenomicEthnicity-Example + - reference: Observation/Observation-NoPregnancy-Example + - reference: >- + FamilyMemberHistory/FamilyMemberHistory-NonConsanguinousUnion-Example + - reference: Observation/Observation-NoTransplant-Example + - reference: Observation/Observation-NoTransfusion-Example + - reference: Condition/Condition-HearingLoss-Example + note: + - text: No family history of genomic testing + - text: >- + Free text for diagnosis/reason for referral, + relevant information including family history, + phenotypic details/ HPO Terms/Patient in need of + test...example + request: + method: POST + url: ServiceRequest + - fullUrl: >- + http://example.org/fhir/Observation/Observation-NoPregnancy-Example + resource: + resourceType: Observation + id: Observation-NoPregnancy-Example + status: final + code: + coding: + - system: http://snomed.info/sct + code: '77386006' + display: Pregnancy + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + effectiveDateTime: '2023-08-05' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-DiseaseStatus-Example + resource: + resourceType: Observation + id: Observation-DiseaseStatus-Example + status: final + code: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R67.2 + display: Monogenic hearing loss + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + effectiveDateTime: '2023-08-05' + valueCodeableConcept: + coding: + - system: http://snomed.info/sct + code: '103310001' + display: Patient not affected + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/FamilyMemberHistory/FamilyMemberHistory-NonConsanguinousUnion-Example + resource: + resourceType: FamilyMemberHistory + id: FamilyMemberHistory-NonConsanguinousUnion-Example + extension: + - url: >- + http://hl7.org/fhir/StructureDefinition/family-member-history-genetics-observation + valueReference: + reference: >- + Observation/Observation-NonConsanguinousUnion-Example + status: completed + patient: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + relationship: + coding: + - system: >- + http://terminology.hl7.org/CodeSystem/v3-RoleCode + code: PRN + display: parent + request: + method: POST + url: FamilyMemberHistory + - fullUrl: >- + http://example.org/fhir/Observation/Observation-NonConsanguinousUnion-Example + resource: + resourceType: Observation + id: Observation-NonConsanguinousUnion-Example + status: final + code: + coding: + - system: http://snomed.info/sct + code: '842009' + display: Consanguinity + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + effectiveDateTime: '2023-08-05' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-NoTransplant-Example + resource: + resourceType: Observation + id: Observation-NoTransplant-Example + status: final + code: + coding: + - system: http://snomed.info/sct + code: '77465005' + display: Transplantation + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + effectiveDateTime: '2023-08-05' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-NoTransfusion-Example + resource: + resourceType: Observation + id: Observation-NoTransfusion-Example + status: final + code: + coding: + - system: http://snomed.info/sct + code: '5447007' + display: Transfusion + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + effectiveDateTime: '2023-08-05' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Condition/Condition-HearingLoss-Example + resource: + resourceType: Condition + id: Condition-HearingLoss-Example + code: + coding: + - system: http://snomed.info/sct + code: '95820000' + display: Bilateral hearing loss + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + note: + - text: hearing loss since childhood (example) + request: + method: POST + url: Condition + - fullUrl: >- + http://example.org/fhir/Specimen/Specimen-BloodEDTA-Example + resource: + resourceType: Specimen + id: Specimen-BloodEDTA-Example + identifier: + - system: https://fhir.add.nhs.uk/Id/specimenId + value: RGT03135 + status: unavailable + type: + coding: + - system: http://snomed.info/sct + code: '445295009' + display: Blood specimen with EDTA + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + request: + - reference: >- + ServiceRequest/ServiceRequest-NonWGSTestOrderForm-Example + request: + method: POST + url: Specimen + WGS-Test-Request-Rare-Disease: + summary: Bundle-WGSTestOrderForm-Example + description: >- + Example + [transaction](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/Examples/Bundle/Bundle-WGSTestOrderForm-Example) + of a Non-WGS test request sent to the central broker, as + described in the Clinica Scenario [**WGS-Test-Request - + Rare-Disease**](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/Design/Clinical-Scenarios#WGS-Test-Request---Rare-Disease). + value: + resourceType: Bundle + id: Bundle-WGSTestOrderForm-Example + type: transaction + entry: + - fullUrl: >- + http://example.org/fhir/PractitionerRole/PractitionerRole-HazelSmithRenal-Example + resource: + resourceType: PractitionerRole + id: PractitionerRole-HazelSmithRenal-Example + practitioner: + identifier: + system: https://fhir.nhs.uk/Id/sds-user-id + value: '9999999998' + display: Dr. Hazel Smith + organization: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RAX01 + display: Kingston Hospital NHS Foundation Trust + specialty: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-PracticeSettingCode + code: '361' + display: Renal Medicine + telecom: + - system: phone + value: '02085467711' + - system: email + value: Hazel.smith12@nhs.net + - system: email + value: renalseckingston@nhs.net + extension: + - url: >- + http://hl7.org/fhir/StructureDefinition/contactpoint-comment + valueString: reporting + request: + method: POST + url: PractitionerRole + - fullUrl: >- + http://example.org/fhir/Patient/Patient-LindsaySorrell-Example + resource: + resourceType: Patient + id: Patient-LindsaySorrell-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BirthSex + valueCodeableConcept: + coding: + - system: >- + http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender + code: M + display: Male + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-EthnicCategory + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-EthnicCategoryEngland + code: A + display: White - British + identifier: + - system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-NHSNumberVerificationStatus + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-NHSNumberVerificationStatusEngland + version: 2.2.0 + code: '01' + display: Number present and verified + - system: urn:oid:2.XX.XXX.X.XXXXXX.X.X.X.X.X.18.24 + value: RWT14789 + assigner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RAX01 + name: + - given: + - Lindsay + family: Sorrell + gender: male + birthDate: '2011-04-12' + deceasedBoolean: false + address: + - line: + - 31 THE AVENUE + - BERWICK COURT + postalCode: KT4 7BS + generalPractitioner: + - identifier: + system: https://fhir.hl7.org.uk/Id/gmp-number + value: G9999999 + display: Dr. Aero Smith + - identifier: + system: https://fhir.hl7.org.uk/Id/ODS-code + value: AP123 + display: anywhere place + link: + - other: + reference: >- + https://api.service.nhs.uk/personal-demographics/FHIR/R4/Patient/9449307946 + type: seealso + request: + method: POST + url: Patient + ifNoneExist: >- + Patient?identifier=https://fhir.nhs.uk/Id/nhs-number|9449307946 + - fullUrl: >- + http://example.org/fhir/Observation/Observation-GenomicEthnicity-Example + resource: + resourceType: Observation + id: Observation-GenomicEthnicity-Example + status: preliminary + code: + coding: + - system: http://snomed.info/sct + code: '723621000000103' + display: Ethnicity + subject: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + valueString: unknown + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderForm-Example + resource: + resourceType: ServiceRequest + id: ServiceRequest-WGSTestOrderForm-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory + code: nhs + display: NHS + status: active + intent: order + category: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory + code: rare-disease-wgs + display: Rare Disease - WGS + priority: routine + code: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R193.4 + display: Cystic renal disease + subject: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + authoredOn: '2023-08-08' + requester: + reference: >- + PractitionerRole/PractitionerRole-HazelSmithRenal-Example + reasonCode: + - coding: + - system: http://snomed.info/sct + code: '103693007' + display: Diagnostic procedure + supportingInfo: + - reference: Observation/Observation-DiseaseStatus-Example + - reference: Observation/Observation-GenomicEthnicity-Example + - reference: Observation/Observation-NoPregnancy-Example + - reference: >- + FamilyMemberHistory/FamilyMemberHistory-NonConsanguinousUnion-Example + - reference: >- + Observation/Observation-NoBoneMarrowTransplant-Example + - reference: Observation/Observation-NoTransfusion-Example + - reference: Observation/Observation-MultipleRenalCysts-Example + - reference: Observation/Observation-Nephronophthisis-Example + - reference: Observation/Observation-HepaticCysts-Example + - reference: Observation/Observation-EnlargedKidney-Example + - reference: Observation/Observation-RenalInsufficiency-Example + - reference: Consent/Consent-RoDToFollow-Example + note: + - text: No family history of genomic testing + - text: >- + Free text for diagnosis/reason for referral, + relevant information including family history, + phenotypic details/ HPO Terms/ Patient diagnoses + with ADPKD (example) + request: + method: POST + url: ServiceRequest + - fullUrl: >- + http://example.org/fhir/Observation/Observation-NoPregnancy-Example + resource: + resourceType: Observation + id: Observation-NoPregnancy-Example + status: final + code: + coding: + - system: http://snomed.info/sct + code: '77386006' + display: Pregnancy + subject: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + effectiveDateTime: '2023-08-05' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-DiseaseStatus-Example + resource: + resourceType: Observation + id: Observation-DiseaseStatus-Example + status: final + code: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R193.4 + display: Cystic renal disease + subject: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + effectiveDateTime: '2023-08-05' + valueCodeableConcept: + coding: + - system: http://snomed.info/sct + code: '103310001' + display: Patient not affected + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/FamilyMemberHistory/FamilyMemberHistory-NonConsanguinousUnion-Example + resource: + resourceType: FamilyMemberHistory + id: FamilyMemberHistory-NonConsanguinousUnion-Example + extension: + - url: >- + http://hl7.org/fhir/StructureDefinition/family-member-history-genetics-observation + valueReference: + reference: >- + Observation/Observation-NonConsanguinousUnion-Example + status: completed + patient: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + relationship: + coding: + - system: >- + http://terminology.hl7.org/CodeSystem/v3-RoleCode + code: PRN + display: parent + request: + method: POST + url: FamilyMemberHistory + - fullUrl: >- + http://example.org/fhir/Observation/Observation-NonConsanguinousUnion-Example + resource: + resourceType: Observation + id: Observation-NonConsanguinousUnion-Example + status: final + code: + coding: + - system: http://snomed.info/sct + code: '842009' + display: Consanguinity + subject: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + effectiveDateTime: '2023-08-05' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-NoBoneMarrowTransplant-Example + resource: + resourceType: Observation + id: Observation-NoBoneMarrowTransplant-Example + status: final + code: + coding: + - system: http://snomed.info/sct + code: '23719005' + display: Transplantation of bone marrow + subject: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + effectiveDateTime: '2023-08-05' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-NoTransfusion-Example + resource: + resourceType: Observation + id: Observation-NoTransfusion-Example + status: final + code: + coding: + - system: http://snomed.info/sct + code: '5447007' + display: Transfusion + subject: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + effectiveDateTime: '2023-08-05' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-MultipleRenalCysts-Example + resource: + resourceType: Observation + id: Observation-MultipleRenalCysts-Example + status: final + code: + coding: + - system: https://hpo.jax.org/app/ + code: HP:0005562 + display: Multiple renal cysts + subject: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + effectiveDateTime: '2023-08-05' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-Nephronophthisis-Example + resource: + resourceType: Observation + id: Observation-Nephronophthisis-Example + status: final + code: + coding: + - system: https://hpo.jax.org/app/ + code: HP:0000090 + display: Nephronophthisis + subject: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + effectiveDateTime: '2023-08-05' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-HepaticCysts-Example + resource: + resourceType: Observation + id: Observation-HepaticCysts-Example + status: final + code: + coding: + - system: https://hpo.jax.org/app/ + code: HP:0001407 + display: Hepatic cysts + subject: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + effectiveDateTime: '2023-08-05' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-EnlargedKidney-Example + resource: + resourceType: Observation + id: Observation-EnlargedKidney-Example + status: final + code: + coding: + - system: https://hpo.jax.org/app/ + code: HP:0000105 + display: Enlarged kidney + subject: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + effectiveDateTime: '2023-08-05' + valueBoolean: true + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-RenalInsufficiency-Example + resource: + resourceType: Observation + id: Observation-RenalInsufficiency-Example + status: final + code: + coding: + - system: https://hpo.jax.org/app/ + code: HP:0000083 + display: Renal insufficiency + subject: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + effectiveDateTime: '2023-08-05' + valueBoolean: true + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Specimen/Specimen-BloodEDTA-Example + resource: + resourceType: Specimen + id: Specimen-BloodEDTA-Example + identifier: + - system: https://fhir.add.nhs.uk/Id/specimenId + value: RGT03135 + status: unavailable + type: + coding: + - system: http://snomed.info/sct + code: '445295009' + display: Blood specimen with EDTA + subject: + reference: Patient/Patient-LindsaySorrell-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307946' + request: + - reference: >- + ServiceRequest/ServiceRequest-NonWGSTestOrderForm-Example + request: + method: POST + url: Specimen + - fullUrl: >- + http://example.org/fhir/Consent/Consent-RoDToFollow-Example + resource: + resourceType: Consent + id: Consent-RoDToFollow-Example + status: proposed + scope: + coding: + - system: >- + http://terminology.hl7.org/CodeSystem/consentscope + code: research + display: Research + category: + - coding: + - system: >- + http://terminology.hl7.org/CodeSystem/consentcategorycodes + code: research + display: Research Information Access + policy: + - authority: https://www.england.nhs.uk + uri: >- + https://www.england.nhs.uk/publication/nhs-genomic-medicine-service-record-of-discussion-form + request: + method: POST + url: Consent + Re-analysis-R387: + summary: Bundle-NonWGSTestOrderForm-Reanalysis-Example + description: >- + Example + [transaction](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/Examples/Bundle#Bundle-NonWGSTestOrderForm-Reanalysis-Example) + of a Non-WGS test request sent to the central broker, as + described in the Clinica Scenario + [**Re-analysis-R387**](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/Design/Clinical-Scenarios#Re-analysis--R387). + value: + resourceType: Bundle + id: Bundle-NonWGSTestOrderForm-Reanalysis-Example + type: transaction + entry: + - fullUrl: >- + http://example.org/fhir/PractitionerRole/PractitionerRole-HazelSmithRenal-Example + resource: + resourceType: PractitionerRole + id: PractitionerRole-HazelSmithRenal-Example + practitioner: + identifier: + system: https://fhir.nhs.uk/Id/sds-user-id + value: '9999999998' + display: Dr. Hazel Smith + organization: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RAX01 + display: Kingston Hospital NHS Foundation Trust + specialty: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-PracticeSettingCode + code: '361' + display: Renal Medicine + telecom: + - system: phone + value: '02085467711' + - system: email + value: Hazel.smith12@nhs.net + - system: email + value: renalseckingston@nhs.net + extension: + - url: >- + http://hl7.org/fhir/StructureDefinition/contactpoint-comment + valueString: reporting + - system: email + value: neuroseckingston@nhs.net + extension: + - url: >- + http://hl7.org/fhir/StructureDefinition/contactpoint-comment + valueString: reporting + request: + method: POST + url: PractitionerRole + - fullUrl: >- + http://example.org/fhir/Patient/Patient-DemeizaSeo-Example + resource: + resourceType: Patient + id: Patient-DemeizaSeo-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BirthSex + valueCodeableConcept: + coding: + - system: >- + http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender + code: F + display: Female + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-EthnicCategory + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-EthnicCategoryEngland + code: R + display: Other Ethnic Groups - Chinese + identifier: + - system: https://fhir.nhs.uk/Id/nhs-number + value: '9449306559' + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-NHSNumberVerificationStatus + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-NHSNumberVerificationStatusEngland + version: 2.2.0 + code: '01' + display: Number present and verified + - system: urn:oid:2.XX.XXX.X.XXXXXX.X.X.X.X.X.18.24 + value: RWT16378 + assigner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RAX + name: + - given: + - Demeiza + family: Seo + gender: female + birthDate: '2011-01-26' + deceasedBoolean: false + address: + - line: + - 1 Aragon Avenue, + - Thames Ditton + city: Surrey + postalCode: KT7 0PY + generalPractitioner: + - identifier: + system: https://fhir.hl7.org.uk/Id/gmp-number + value: G9999999 + display: Dr. Aero Smith + - identifier: + system: https://fhir.hl7.org.uk/Id/ODS-code + value: TP123 + display: 123 Test Practice + link: + - other: + reference: >- + https://api.service.nhs.uk/personal-demographics/FHIR/R4/Patient/9449307559 + type: seealso + request: + method: POST + url: Patient + ifNoneExist: >- + Patient?identifier=https://fhir.nhs.uk/Id/nhs-number|9449307559 + - fullUrl: >- + http://example.org/fhir/Observation/Observation-GenomicEthnicity-Example + resource: + resourceType: Observation + id: Observation-GenomicEthnicity-Example + status: preliminary + code: + coding: + - system: http://snomed.info/sct + code: '723621000000103' + display: Ethnicity + subject: + reference: Patient/Patient-DemeizaSeo-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307559' + valueString: unknown + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/ServiceRequest/ServiceRequest-NonWGSTestOrderForm-ReAnalysis-Example + resource: + resourceType: ServiceRequest + id: ServiceRequest-NonWGSTestOrderForm-ReAnalysis-Example + basedOn: + - reference: >- + ServiceRequest/ServiceRequest-NonWGSTestOrderForm-SyndromicEpilepsy-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory + code: nhs + display: NHS + status: active + intent: order + category: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory + code: rare-disease-non-wgs + priority: routine + code: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R387 + display: Re-analysis + orderDetail: + - coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R59 + display: Early onset or syndromic epilepsy + subject: + reference: Patient/Patient-DemeizaSeo-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449306559' + authoredOn: '2023-09-06T09:00:00Z' + requester: + reference: >- + PractitionerRole/PractitionerRole-HazelSmithRenal-Example + reasonCode: + - coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: '719641000000101' + display: Data analysis (qualifier value) + text: >- + Significant new treatment and or clinical + management implication for the patient.Please + provide details/treatment for management of + epilepsy + supportingInfo: + - reference: Observation/Observation-GenomicEthnicity-Example + - reference: Observation/Observation-DiseaseStatus-Example + - reference: Observation/Observation-NoPregnancy-Example + - reference: >- + Observation/Observation-NonConsanguinousUnion-Example + - reference: >- + FamilyMemberHistory/FamilyMemberHistory-NonConsanguinousUnion-Example + - reference: >- + Observation/Observation-NoBoneMarrowTransplant-Example + - reference: Observation/Observation-NoTransfusion-Example + specimen: + - display: No Sample Required + note: + - text: No family history of genomic testing + - text: >- + Free text for diagnosis/reason for referral, + relevant information including family history, + phenotypic details/ HPO Terms/E.g. Reanlaysis - + change in observed phenotype. Epilepsy test + previously ordered on patient 5 years ago. + request: + method: POST + url: ServiceRequest + - fullUrl: >- + http://example.org/fhir/Observation/Observation-NoPregnancy-Example + resource: + resourceType: Observation + id: Observation-NoPregnancy-Example + status: final + code: + coding: + - system: http://snomed.info/sct + code: '77386006' + display: Pregnancy + subject: + reference: Patient/Patient-DemeizaSeo-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307559' + effectiveDateTime: '2023-09-06' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-DiseaseStatus-Example + resource: + resourceType: Observation + id: Observation-DiseaseStatus-Example + status: final + code: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R67.2 + display: Monogenic hearing loss + subject: + reference: Patient/Patient-DemeizaSeo-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307559' + effectiveDateTime: '2023-09-06' + valueCodeableConcept: + coding: + - system: http://snomed.info/sct + code: '103310001' + display: Patient not affected + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/FamilyMemberHistory/FamilyMemberHistory-NonConsanguinousUnion-Example + resource: + resourceType: FamilyMemberHistory + id: FamilyMemberHistory-NonConsanguinousUnion-Example + extension: + - url: >- + http://hl7.org/fhir/StructureDefinition/family-member-history-genetics-observation + valueReference: + reference: >- + Observation/Observation-NonConsanguinousUnion-Example + status: completed + patient: + reference: Patient/Patient-DemeizaSeo-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307559' + relationship: + coding: + - system: >- + http://terminology.hl7.org/CodeSystem/v3-RoleCode + code: PRN + display: parent + request: + method: POST + url: FamilyMemberHistory + - fullUrl: >- + http://example.org/fhir/Observation/Observation-NonConsanguinousUnion-Example + resource: + resourceType: Observation + id: Observation-NonConsanguinousUnion-Example + status: final + code: + coding: + - system: http://snomed.info/sct + code: '842009' + display: Consanguinity + subject: + reference: Patient/Patient-DemeizaSeo-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307559' + effectiveDateTime: '2023-09-06' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-NoBoneMarrowTransplant-Example + resource: + resourceType: Observation + id: Observation-NoBoneMarrowTransplant-Example + status: final + code: + coding: + - system: http://snomed.info/sct + code: '23719005' + display: Transplantation of bone marrow + subject: + reference: Patient/Patient-DemeizaSeo-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307559' + effectiveDateTime: '2023-08-05' + valueBoolean: false + request: + method: POST + url: Observation + - fullUrl: >- + http://example.org/fhir/Observation/Observation-NoTransfusion-Example + resource: + resourceType: Observation + id: Observation-NoTransfusion-Example + status: final + code: + coding: + - system: http://snomed.info/sct + code: '5447007' + display: Transfusion + subject: + reference: Patient/Patient-DemeizaSeo-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307559' + effectiveDateTime: '2023-09-06' + valueBoolean: false + request: + method: POST + url: Observation + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-service-request-post' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + get: + operationId: getSearchPages + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Get results pages + description: > + ## Overview + This endpoint allows you to retrieve the records of based on pagination parameters. + tags: + - process + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/GetPages' + - $ref: '#/components/parameters/GetPageOffset' + - $ref: '#/components/parameters/Count' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-servicerequests-get' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/ServiceRequest: + get: + operationId: getServiceRequests + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Search for ServiceRequests + description: > + ## Overview + + This endpoint allows you to retrieve the records of ServiceRequests + using various query parameters. Refer [search](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/Build/Supported-CRUD-capability#Read) for more details. + + ## UGR - Search for patient genomic test requests. + tags: + - order + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/PatientIdentifier' + - $ref: '#/components/parameters/LogicalIdentifier' + - $ref: '#/components/parameters/Identifier' + - $ref: '#/components/parameters/Authored' + - $ref: '#/components/parameters/Requestor' + - $ref: '#/components/parameters/Performer' + - $ref: '#/components/parameters/Status' + - $ref: '#/components/parameters/Category' + - $ref: '#/components/parameters/TestID' + - $ref: '#/components/parameters/Include' + - $ref: '#/components/parameters/RevInclude' + - $ref: '#/components/parameters/SupportingInfo' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-servicerequests-get' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/ServiceRequest/{id}/$graph: + get: + operationId: getservicerequestinformation + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Get detailed information around a service request. + description: > + This endpoint allows to retrieve all related records of a ServiceRequest + + using logical identifier and [graph + definition](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/GraphDefinitions) + on the server. + tags: + - order + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/Id' + - $ref: '#/components/parameters/Graph' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-servicerequests-get' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/RequestGroup: + get: + operationId: getRequestGroup + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Search for RequestGroup + description: > + ## Overview + + This endpoint allows you to retrieve the records of RequestGroup + using various query parameters. Refer [search](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/Build/Supported-CRUD-capability#Read) for more details. + + tags: + - order + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/PatientIdentifier' + - $ref: '#/components/parameters/LogicalIdentifier' + - $ref: '#/components/parameters/Identifier' + - $ref: '#/components/parameters/Status' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-servicerequests-get' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/RequestGroup/{id}/$graph: + get: + operationId: getrequestgroupinformation + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Get detailed information around a Request Group. + description: > + This endpoint allows to retrieve all related records of a ServiceRequest + + using logical identifier and [graph + definition](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/GraphDefinitions) + on the server. + tags: + - order + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/Id' + - $ref: '#/components/parameters/GraphRequestGroup' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-servicerequests-get' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/Task: + get: + operationId: getTasks + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Search for Tasks + description: > + ## Overview + + This endpoint allows you to retrieve the records of Tasks using various + query parameters. Refer [search](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/Build/Supported-CRUD-capability#Read) for more details. + tags: + - task + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/PatientIdentifier' + - $ref: '#/components/parameters/LogicalIdentifier' + - $ref: '#/components/parameters/TaskAuthored' + - $ref: '#/components/parameters/Requestor' + - $ref: '#/components/parameters/Owner' + - $ref: '#/components/parameters/Status' + - $ref: '#/components/parameters/TaskCode' + - $ref: '#/components/parameters/BusinessStatus' + - $ref: '#/components/parameters/TaskInclude' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-tasks-get' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/DiagnosticReport: + get: + operationId: getDiagnosticReports + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Search for DiagnosticReports + description: > + ## Overview + + This endpoint allows you to retrieve the records of DiagnosticReport + using various query parameters. Refer [search](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/Build/Supported-CRUD-capability#Read) for more details. + + ## UGR - Search for patient test reports. + tags: + - report + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/PatientIdentifier' + - $ref: '#/components/parameters/LogicalIdentifier' + - $ref: '#/components/parameters/Identifier' + - $ref: '#/components/parameters/BasedOn' + - $ref: '#/components/parameters/ReportIssued' + - $ref: '#/components/parameters/Performer' + - $ref: '#/components/parameters/ResultsInterpreter' + - $ref: '#/components/parameters/Status' + - $ref: '#/components/parameters/DiagnosticReportInclude' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-diagnosticreports-get' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/DiagnosticReport/{id}/$graph: + get: + operationId: getdiagnosticreportinformation + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Get detailed information around a diagnostic report. + description: > + This endpoint allows to retrieve all related records of a DiagnosticReport + + using logical identifier and [graph + definition](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/GraphDefinitions) + on the server. + tags: + - report + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/Id' + - $ref: '#/components/parameters/GraphReport' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-diagnosticreports-get' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/Specimen: + get: + operationId: getSpecimens + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Search for Specimens + description: > + ## Overview + + This endpoint allows you to retrieve the records of Specimens using + various query parameters. Refer [search](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/Build/Supported-CRUD-capability#Read) for more details. + tags: + - specimen + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/PatientIdentifier' + - $ref: '#/components/parameters/LogicalIdentifier' + - $ref: '#/components/parameters/Identifier' + - $ref: '#/components/parameters/SpecimenRequest' + - $ref: '#/components/parameters/SpecimenCollected' + - $ref: '#/components/parameters/ContainerIdentifier' + - $ref: '#/components/parameters/Status' + - $ref: '#/components/parameters/SpecimenInclude' + - $ref: '#/components/parameters/SpecimenRevInclude' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-specimens-get' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/Patient: + get: + operationId: getPatient + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Search for Patient + description: > + ## Overview + + This endpoint allows you to retrieve the record of a patient held within genomic order management service using various query parameters. Refer [search](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/Build/Supported-CRUD-capability#Read) for more details. + + ## UGR - Search for patient genomic record + tags: + - patient + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/LogicalIdentifier' + - $ref: '#/components/parameters/Identifier' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-patient-get' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/RelatedPerson: + get: + operationId: getRelatedPerson + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Search for RelatedPerson + description: > + ## Overview + + This endpoint allows you to retrieve the record of a RelatedPerson + held within genomic order management service using various query + parameters. Refer [search](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/Build/Supported-CRUD-capability#Read) for more details. + tags: + - relatedperson + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/LogicalIdentifier' + - $ref: '#/components/parameters/Identifier' + - $ref: '#/components/parameters/PatientIdentifier' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-relatedperson-get' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/PractitionerRole: + get: + operationId: getPractitionerRole + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Search for PractitionerRole + description: > + ## Overview + + This endpoint allows you to retrieve the record of a PractitionerRole + held within genomic order management service using various query + parameters. Refer [search](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/Build/Supported-CRUD-capability#Read) for more details. + tags: + - practitionerrole + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/LogicalIdentifier' + - $ref: '#/components/parameters/PractitionerIdentifier' + - $ref: '#/components/parameters/Organisation' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-practitionerrole-get' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/{resourceName}/$validate: + post: + operationId: validategenomicrequests + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Validate genomic test requests resource without processing them for storage + description: > + ## Overview + + This endpoint allows you to validate a genomics test resource without processing for storage with backend infrastructure. + tags: + - process + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/ResourceName' + responses: + '200': + $ref: >- + #/components/responses/200-goms-bundle-practitionerrole-get-logical-id + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/{resourceName}/{id}: + get: + operationId: readResource + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Search for resource by its logical id + description: > + ## Overview + + This endpoint allows you to retrieve the record of a single FHIR + resource latest version by its logical id. + tags: + - history + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/ResourceName' + - $ref: '#/components/parameters/Id' + responses: + '200': + $ref: >- + #/components/responses/200-goms-bundle-practitionerrole-get-logical-id + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/{resourceName}/{id}/_history: + get: + summary: Retrieve resource history by its logical id + operationId: readResourceHistory + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + description: > + ## Overview + + This endpoint allows you to retrieve the full history of a single FHIR + resource by its logical id. + + + ## Sandbox testing + + You can test the following scenarios in our sandbox environment: + + + | Scenario | + Request + | + Response + | + + | ----------------------------------------| + ----------------------------------------------------------------------------------------------------------------------------------------------------------------| + ------------------------------------------------------------------------| + + | + | + | + | + tags: + - history + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/ResourceName' + - $ref: '#/components/parameters/Id' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-service-request-history' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/{resourceName}/{id}/_history/{versionId}: + get: + summary: Retrieve Resource version by its logical id + operationId: readResourceHistoryVersion + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + description: > + ## Overview + + This endpoint allows you to retrieve a single resource specified version + by its logical id. + + + ## Sandbox testing + + You can test the following scenarios in our sandbox environment: + + + | Scenario | + Request + | + Response + | + + | ----------------------------------------| + ----------------------------------------------------------------------------------------------------------------------------------------------------------------| + ------------------------------------------------------------------------| + + | + | + | + | + tags: + - history + parameters: + - $ref: '#/components/parameters/apikey' + - $ref: '#/components/parameters/NHSDSessionURID' + - $ref: '#/components/parameters/RequestID' + - $ref: '#/components/parameters/CorrelationID' + - $ref: '#/components/parameters/ResourceName' + - $ref: '#/components/parameters/Id' + - $ref: '#/components/parameters/VersionId' + responses: + '200': + $ref: '#/components/responses/200-goms-bundle-service-request-read' + 4XX: + $ref: '#/components/responses/4XX-goms-error' + /FHIR/R4/metadata: + get: + operationId: readMetadata + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] + summary: Get the capability statement from server + description: > + ## Overview + + This endpoint allows to retrieve the [capability statement](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/CapabilityStatements) from server + tags: + - meta + parameters: + - $ref: '#/components/parameters/apikey' + responses: + '200': + description : 'Successful retrieval of metadata.' +components: + securitySchemes: + app-level0: + $ref: >- + https://proxygen.prod.api.platform.nhs.uk/components/securitySchemes/app-level0 + app-level3: + $ref: >- + https://proxygen.prod.api.platform.nhs.uk/components/securitySchemes/app-level3 + nhs-cis2-aal3: + $ref: >- + https://proxygen.ptl.api.platform.nhs.uk/components/securitySchemes/nhs-cis2-aal3 + responses: + 4XX-goms-error: + description: > + Below are examples of potential HTTP status codes and their associated + error codes, which could be returned in the event of a fault. + + + | HTTP status | Error code | Description | + + | ----------- | -------------------------- | + --------------------------------------------- | + + | 400 | INVALID | The provided event ID is + either missing or not in the expected format. | + + | 400 | BAD_REQUEST | Search could not be + processed or failed basic FHIR validation rules | + + | 401 | UNAUTHORISED | Authorization is required + for the interaction that was attempted | + + | 400 | BAD_REQUEST | The resource could not be + parsed or failed basic FHIR validation rules | + + | 404 | NOT_FOUND | The requested resource was + not found. | + + | 405 | NOT_ALLOWED | The requested method is not + allowed | + + | 422 | UNPROCESSABLE_ENTITY | The proposed resource + violated applicable FHIR profiles or server business rules. This should + be accompanied by an OperationOutcome resource providing additional + detail | + content: + application/fhir+json: + schema: + type: object + description: > + Outcome of an operation that does not result in a resource or + bundle being returned (for example, error, async/batch + submission). + properties: + resourceType: + type: string + description: FHIR Resource Type. + enum: + - OperationOutcome + example: OperationOutcome + issue: + type: array + description: List of issues that have occurred. + minItems: 1 + items: + type: object + required: + - severity + - code + properties: + severity: + type: string + enum: + - fatal + - error + - warning + - information + description: Severity of the error. + example: error + code: + type: string + description: FHIR error code. + example: invalid + enum: + - invalid + - structure + - required + - value + - invariant + - security + - login + - unknown + - expired + - forbidden + - suppressed + - processing + - not-supported + - duplicate + - multiple-matches + - not-found + - deleted + - too-long + - code-invalid + - extension + - too-costly + - business-rule + - conflict + - transient + - lock-error + - no-store + - exception + - timeout + - incomplete + - throttled + - informational + details: + type: object + description: Internal error code. + properties: + coding: + type: array + items: + type: object + required: + - system + - code + properties: + system: + type: string + description: URI of the coding system specification. + enum: + - >- + https://fhir.nhs.uk/R4/CodeSystem/Spine-ErrorOrWarningCode + code: + type: string + description: Symbol in syntax defined by the system. + example: INVALID_VALUE + display: + type: string + description: Representation defined by the system. + example: Provided value is invalid + diagnostics: + type: string + pattern: '[ \r\n\t\S]+' + description: Additional diagnostic information about the issue. + location: + type: array + items: + type: string + pattern: '[ \r\n\t\S]+' + description: >- + This element is deprecated because it is XML specific. + It is replaced by issue.expression, which is format + independent, and simpler to parse. + + + For resource issues, this will be a simple XPath + limited to element names, repetition indicators and + the default child accessor that identifies one of the + elements in the resource that caused this issue to be + raised. For HTTP errors, will be "http." + the + parameter name. + expression: + type: array + items: + type: string + pattern: '[ \r\n\t\S]+' + description: >- + A [simple subset of FHIRPath](fhirpath.html#simple) + limited to element names, repetition indicators and + the default child accessor that identifies one of the + elements in the resource that caused this issue to be + raised. + examples: + single_item: + description: | + An error response to a request. + value: + resourceType: OperationOutcome + meta: + lastUpdated: '2022-10-21T13:47:00+00:00' + issue: + - severity: error + code: value + details: + coding: + - system: >- + https://fhir.nhs.uk/R4/CodeSystem/Spine-ErrorOrWarningCode + code: MISSING_FIELD + display: ResourceType Bundle must contain 'entry' field + 200-goms-bundle-service-request-post: + description: A response from the /FHIR/R4/ServiceRequest endpoint. + content: + application/fhir+json: + schema: + type: object + description: A response from the /FHIR/R4/ServiceRequest endpoint. + properties: + resourceType: + type: string + description: FHIR Resource Type. + enum: + - OperationOutcome + example: OperationOutcome + issue: + type: array + description: Successfull processing of request. + minItems: 1 + items: + type: object + required: + - severity + - code + properties: + severity: + type: string + enum: + - success + description: Severity set to 'success'. + example: success + code: + type: string + description: FHIR error code. + example: invalid + enum: + - success + details: + type: object + description: Internal error code. + properties: + coding: + type: array + items: + type: object + required: + - text + properties: + text: + type: string + description: URI of the coding system specification. + enum: + - >- + https://fhir.nhs.uk/R4/CodeSystem/Spine-ErrorOrWarningCode + code: + type: string + description: Symbol in syntax defined by the system. + example: INVALID_VALUE + display: + type: string + description: Representation defined by the system. + example: Provided value is invalid + expression: + type: string + description: FHIRPath of element(s) related to the error. + example: Patient.name.given + examples: + single-item: + description: A successful response containing a single outcome item. + value: + resourceType: Bundle + type: transaction-response + entry: + - fullUrl: urn:uuid:4d70678c-81e4-4ff4-8c67-17596fd0aa46 + response: + status: 201 Created + outcome: + resourceType: OperationOutcome + meta: + lastUpdated: '2023-09-11T10:11:12.000Z' + issue: + - severity: success + code: success + diagnostics: No issues detected during validation. + multiple-items: + description: A successful response containing multiple outcome items. + value: + resourceType: Bundle + type: transaction-response + entry: + - fullUrl: urn:uuid:4d70678c-81e4-4ff4-8c67-17596fd0aa46 + response: + status: 201 Created + location: Patient/e87361ea-b6fb-482e-a252-af3199792582/ + outcome: + resourceType: OperationOutcome + meta: + lastUpdated: '2023-09-11T10:11:12.000Z' + issue: + - severity: information + code: success + diagnostics: No issues detected during validation. + - fullUrl: urn:uuid:0ae4daf3-f24b-479d-b8fa-b69e2d873b60 + response: + status: 201 Created + location: ServiceRequest/4d70678c-81e4-4ff4-8c67-17596fd0aa46/ + outcome: + resourceType: OperationOutcome + meta: + lastUpdated: '2023-09-11T10:11:12.000Z' + issue: + - severity: information + code: success + diagnostics: No issues detected during validation. + 20X-goms-bundle-task-create-update: + description: A response from the /FHIR/R4/Task create update action. + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: > + A FHIR + [Task](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Task) + examples: + single-item: + description: Task for creation + value: + resourceType: Task + id: 8322cbf4-8fd0-46ab-bffe-abf39ee7a3f6 + status: cancelled + statusReason: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics + code: TestNoLongerRequired + display: Test No Longer Required + intent: order + priority: routine + code: + coding: + - system: https://fhir.nhs.uk/CodeSystem/task-code-genomics + code: ProcessGenomicTestRequest + display: Process Genomic Test Request + focus: + reference: >- + ServiceRequest/ServiceRequest-NonWGSTestOrderForm-Cancellation-Example + for: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + authoredOn: '2023-08-08T15:43:00Z' + lastModified: '2023-08-08T15:43:00Z' + requester: + reference: PractitionerRole/PractitionerRole-GeneSmithENT-Example + owner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RGT01 + display: ADDENBROOKE'S HOSPITAL + note: null + 20X-goms-bundle-servicerequest-create-update: + description: A response from the /FHIR/R4/Task create update action. + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: > + A FHIR + [Task](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Task) + examples: + single-item: + description: Task for creation + value: + resourceType: ServiceRequest + id: ServiceRequest-NonWGSTestOrderForm-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory + code: nhs + display: NHS + status: active + intent: order + category: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory + code: rare-disease-non-wgs + display: Rare Disease - Non-WGS + priority: routine + code: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R67.2 + display: Monogenic hearing loss + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + authoredOn: '2023-08-05' + requester: + reference: PractitionerRole/PractitionerRole-GeneSmithENT-Example + reasonCode: + - coding: + - system: http://snomed.info/sct + code: '103693007' + display: Diagnostic procedure + supportingInfo: + - reference: Observation/Observation-DiseaseStatus-Example + - reference: Observation/Observation-GenomicEthnicity-Example + - reference: Observation/Observation-NoPregnancy-Example + - reference: >- + FamilyMemberHistory/FamilyMemberHistory-NonConsanguinousUnion-Example + - reference: Observation/Observation-NoTransplant-Example + - reference: Observation/Observation-NoTransfusion-Example + - reference: Condition/Condition-HearingLoss-Example + note: + - text: No family history of genomic testing + - text: >- + Free text for diagnosis/reason for referral, relevant + information including family history, phenotypic details/ + HPO Terms/Patient in need of test...example + 200-goms-bundle-task-post: + description: A response from the /FHIR/R4/Task endpoint. + content: + application/fhir+json: + schema: + type: object + description: A response from the /FHIR/R4/Task endpoint. + properties: + resourceType: + type: string + description: FHIR Resource Type. + enum: + - OperationOutcome + example: OperationOutcome + issue: + type: array + description: Successfull processing of request. + minItems: 1 + items: + type: object + required: + - severity + - code + properties: + severity: + type: string + enum: + - success + description: Severity set to 'success'. + example: success + code: + type: string + description: FHIR error code. + example: invalid + enum: + - success + details: + type: object + description: Internal error code. + properties: + coding: + type: array + items: + type: object + required: + - text + properties: + text: + type: string + description: URI of the coding system specification. + enum: + - >- + https://fhir.nhs.uk/R4/CodeSystem/Spine-ErrorOrWarningCode + code: + type: string + description: Symbol in syntax defined by the system. + example: INVALID_VALUE + display: + type: string + description: Representation defined by the system. + example: Provided value is invalid + expression: + type: string + description: FHIRPath of element(s) related to the error. + example: Patient.name.given + examples: + single-item: + description: >- + A successful response to a task create, contains a single + outcome item. + value: + resourceType: Bundle + type: transaction-response + entry: + - fullUrl: urn:uuid:4d70678c-81e4-4ff4-8c67-17596fd0aa46 + response: + status: 201 Created + outcome: + resourceType: OperationOutcome + meta: + lastUpdated: '2023-09-11T10:11:12.000Z' + issue: + - severity: success + code: success + diagnostics: No issues detected during validation. + 20X-goms-bundle-diagnostic-report-create-update: + description: A response from the /FHIR/R4/DiagnosticReport create update operation + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: > + A FHIR + [DiagnosticReport](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-DiagnosticReport) + examples: + single-item: + description: DiagnosticReport for creation + value: + resourceType: DiagnosticReport + id: ad23e6a8-914a-49d3-842e-f8058f639225 + identifier: + - system: https://www.guysandstthomas.nhs.uk/SEGLH/lims + value: FHGenomicReport + assigner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RJ1 + basedOn: + - reference: >- + ServiceRequest/ServiceRequest-NonWGSTestOrderForm-NewFollowupTest-Example + status: final + category: + - coding: + - system: http://terminology.hl7.org/CodeSystem/v2-0074 + code: GE + display: Genetics + code: + coding: + - system: http://snomed.info/sct + code: '1054161000000101' + display: Genetic report + subject: + reference: Patient/Patient-AnitaLamberts-Example + issued: '2023-11-24T09:45:00Z' + performer: + - identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RJ1 + specimen: + - reference: Specimen/Specimen-BloodEDTA-Example + presentedForm: + - contentType: application/pdf + language: en-GB + url: https://o719on.axshare.com/?id=8aol33&p=introduction&g=1 + size: 43272 + title: Genomic Report for Anita Lamberts + creation: '2023-11-24' + 200-goms-bundle-diagnosticreport-post: + description: A response from the /FHIR/R4/Task endpoint. + content: + application/fhir+json: + schema: + type: object + description: A response from the /FHIR/R4/Task endpoint. + properties: + resourceType: + type: string + description: FHIR Resource Type. + enum: + - OperationOutcome + example: OperationOutcome + issue: + type: array + description: Successfull processing of request. + minItems: 1 + items: + type: object + required: + - severity + - code + properties: + severity: + type: string + enum: + - success + description: Severity set to 'success'. + example: success + code: + type: string + description: FHIR error code. + example: invalid + enum: + - success + details: + type: object + description: Internal error code. + properties: + coding: + type: array + items: + type: object + required: + - text + properties: + text: + type: string + description: URI of the coding system specification. + enum: + - >- + https://fhir.nhs.uk/R4/CodeSystem/Spine-ErrorOrWarningCode + code: + type: string + description: Symbol in syntax defined by the system. + example: INVALID_VALUE + display: + type: string + description: Representation defined by the system. + example: Provided value is invalid + expression: + type: string + description: FHIRPath of element(s) related to the error. + example: Patient.name.given + examples: + single-item: + description: >- + A successful response to a task create, contains a single + outcome item. + value: + resourceType: Bundle + type: transaction-response + entry: + - fullUrl: urn:uuid:4d70678c-81e4-4ff4-8c67-17596fd0aa46 + response: + status: 201 Created + outcome: + resourceType: OperationOutcome + meta: + lastUpdated: '2023-09-11T10:11:12.000Z' + issue: + - severity: success + code: success + diagnostics: No issues detected during validation. + 200-goms-bundle-diagnosticreports-get: + description: | + Read DiagnosticReports operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A FHIR + [bundle](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Bundle) + with collection of [FHIR + DiagnosticReports](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-DiagnosticReport) + examples: + single-item: + description: >- + A successful response to a diagnostic report get, contains a + single item. + value: + resourceType: Bundle + type: searchset + entry: + - resourceType: DiagnosticReport + id: DiagnosticReport-AnitaLamberts-Example + identifier: + - system: https://www.guysandstthomas.nhs.uk/SEGLH/lims + value: FHGenomicReport + assigner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RJ1 + basedOn: + - reference: >- + ServiceRequest/ServiceRequest-NonWGSTestOrderForm-NewFollowupTest-Example + status: final + category: + - coding: + - system: http://terminology.hl7.org/CodeSystem/v2-0074 + code: GE + display: Genetics + code: + coding: + - system: http://snomed.info/sct + code: '1054161000000101' + display: Genetic report + subject: + reference: Patient/Patient-AnitaLamberts-Example + issued: '2023-11-24T09:45:00Z' + performer: + - identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RJ1 + specimen: + - reference: Specimen/Specimen-BloodEDTA-Example + presentedForm: + - contentType: application/pdf + language: en-GB + url: >- + https://o719on.axshare.com/?id=8aol33&p=introduction&g=1 + size: 43272 + title: Genomic Report for Anita Lamberts + creation: '2023-11-24' + multiple-items: + description: >- + A successful response to a diagnos report get, contains a + multiple items. + value: + resourceType: Bundle + type: searchset + entry: + - resourceType: DiagnosticReport + id: DiagnosticReport-AnitaLamberts-Example + identifier: + - system: https://www.guysandstthomas.nhs.uk/SEGLH/lims + value: FHGenomicReport + assigner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RJ1 + basedOn: + - reference: >- + ServiceRequest/ServiceRequest-NonWGSTestOrderForm-NewFollowupTest-Example + status: final + category: + - coding: + - system: http://terminology.hl7.org/CodeSystem/v2-0074 + code: GE + display: Genetics + code: + coding: + - system: http://snomed.info/sct + code: '1054161000000101' + display: Genetic report + subject: + reference: Patient/Patient-AnitaLamberts-Example + issued: '2023-11-24T09:45:00Z' + performer: + - identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RJ1 + specimen: + - reference: Specimen/Specimen-BloodEDTA-Example + presentedForm: + - contentType: application/pdf + language: en-GB + url: >- + https://o719on.axshare.com/?id=8aol33&p=introduction&g=1 + size: 43272 + title: Genomic Report for Anita Lamberts + creation: '2023-11-24' + - resourceType: DiagnosticReport + id: DiagnosticReport-FayMutlowGeneticReport-Example + identifier: + - system: https://newcastle-hospitsls.nhs.uk/nwglh/lims + value: FHGenomicReport + assigner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RTD + basedOn: + - reference: >- + ServiceRequest/ServiceRequest-SavedTestOrderUpdated-CascadeTesting-Example + status: final + category: + - coding: + - system: http://terminology.hl7.org/CodeSystem/v2-0074 + code: GE + display: Genetics + code: + coding: + - system: http://snomed.info/sct + code: '1054161000000101' + display: Genetic report + subject: + reference: Patient/Patient-FayMutlow-Example + issued: '2023-10-09T09:45:00Z' + performer: + - identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RTD + specimen: + - reference: Specimen/Specimen-FayMutlowBloodEDTA-Example + conclusionCode: + - coding: + - system: http://snomed.info/sct + code: '398036000' + display: Familial hypercholesterolemia + presentedForm: + - contentType: application/pdf + language: en-GB + url: https://ytlqh0.axshare.com/?id=swl7sq&p=view_report + size: 43272 + title: Genomic Report for Fay Mutlow + creation: '2023-10-22' + 200-goms-bundle-tasks-get: + description: | + Read tasks operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A FHIR + [bundle](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Bundle) + with collection of [FHIR + Tasks](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Task) + examples: + single-item: + description: A successful response to a task get, contains a single item. + value: + resourceType: Bundle + type: searchset + entry: + - resourceType: Task + id: Task-NonWGSRareDiseaseTestOrder-Cancellation-Example + status: cancelled + statusReason: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics + code: TestNoLongerRequired + display: Test No Longer Required + intent: order + priority: routine + code: + coding: + - system: https://fhir.nhs.uk/CodeSystem/task-code-genomics + code: ProcessGenomicTestRequest + display: Process Genomic Test Request + focus: + reference: >- + ServiceRequest/ServiceRequest-NonWGSTestOrderForm-Cancellation-Example + for: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + authoredOn: '2023-08-08T15:43:00Z' + lastModified: '2023-08-08T15:43:00Z' + requester: + reference: PractitionerRole/PractitionerRole-GeneSmithENT-Example + owner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RGT01 + display: ADDENBROOKE'S HOSPITAL + note: + - text: Test no longer required. + multiple-items: + description: A successful response to a task get, contains a multiple items. + value: + resourceType: Bundle + type: searchset + entry: + - resourceType: Task + id: Task-NonWGSRareDiseaseTestOrder-Cancellation-Example + status: cancelled + statusReason: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics + code: TestNoLongerRequired + display: Test No Longer Required + intent: order + priority: routine + code: + coding: + - system: https://fhir.nhs.uk/CodeSystem/task-code-genomics + code: ProcessGenomicTestRequest + display: Process Genomic Test Request + focus: + reference: >- + ServiceRequest/ServiceRequest-NonWGSTestOrderForm-Cancellation-Example + for: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + authoredOn: '2023-08-08T15:43:00Z' + lastModified: '2023-08-08T15:43:00Z' + requester: + reference: PractitionerRole/PractitionerRole-GeneSmithENT-Example + owner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RGT01 + display: ADDENBROOKE'S HOSPITAL + note: + - text: Test no longer required. + - resourceType: Task + id: Task-NonWGSRareDiseaseTestOrder-Example + status: requested + intent: order + priority: routine + code: + coding: + - system: https://fhir.nhs.uk/CodeSystem/task-code-genomics + code: ProcessGenomicTestRequest + display: Process Genomic Test Request + focus: + reference: ServiceRequest/ServiceRequest-SavedTestOrder-Example + for: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + authoredOn: '2023-08-05' + requester: + reference: PractitionerRole/PractitionerRole-GeneSmithENT-Example + 200-goms-bundle-specimens-get: + description: | + Read specimens operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A FHIR + [bundle](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Bundle) + with collection of [FHIR + Specimens](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-Specimen) + examples: + single-item: + description: A successful response to a specimen get, contains a single item. + value: + resourceType: Bundle + type: searchset + entry: + - resourceType: Specimen + id: Specimen-BloodEDTA-Example + identifier: + - system: https://fhir.add.nhs.uk/Id/specimenId + value: RGT03135 + status: unavailable + type: + coding: + - system: http://snomed.info/sct + code: '445295009' + display: Blood specimen with EDTA + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + request: + - reference: >- + ServiceRequest/ServiceRequest-NonWGSTestOrderForm-Example + multiple-items: + description: >- + A successful response to a specimen get, contains a multiple + items. + value: + resourceType: Bundle + type: searchset + entry: + - resourceType: Specimen + id: Specimen-BloodEDTA-Example + identifier: + - system: https://fhir.add.nhs.uk/Id/specimenId + value: RGT03135 + status: unavailable + type: + coding: + - system: http://snomed.info/sct + code: '445295009' + display: Blood specimen with EDTA + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + request: + - reference: >- + ServiceRequest/ServiceRequest-NonWGSTestOrderForm-Example + - resourceType: Specimen + id: Specimen-BloodEDTA-WithCollectoinDetails-Example + identifier: + - system: https://fhir.leedsth.nhs.uk//Id/specimenId + value: RR8-696B0-17843 + status: available + type: + coding: + - system: http://snomed.info/sct + code: '445295009' + display: Blood specimen with EDTA + subject: + reference: Patient/Patient-FayMutlow-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307806' + collection: + collector: + identifier: + system: https://fhir.nhs.uk/Id/sds-user-id + value: '9999999998' + display: Phletobomist-Lois Lane + collectedDateTime: '2023-10-05T15:30:00Z' + request: + - reference: >- + ServiceRequest/ServiceRequest-SavedTestOrderUpdated-CascadeTesting-Example + 200-goms-bundle-servicerequests-get: + description: | + Read Service Request operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A FHIR + [bundle](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Bundle) + with collection of [FHIR + ServiceRequests](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-ServiceRequest) + examples: + single-item: + description: >- + A successful response to a service request get, contains a + single item. + value: + resourceType: Bundle + type: searchset + entry: + - resourceType: ServiceRequest + id: ServiceRequest-NonWGSTestOrderForm-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory + code: nhs + display: NHS + status: active + intent: order + category: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory + code: rare-disease-non-wgs + display: Rare Disease - Non-WGS + priority: routine + code: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R67.2 + display: Monogenic hearing loss + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + authoredOn: '2023-08-05' + requester: + reference: PractitionerRole/PractitionerRole-GeneSmithENT-Example + reasonCode: + - coding: + - system: http://snomed.info/sct + code: '103693007' + display: Diagnostic procedure + supportingInfo: + - reference: Observation/Observation-DiseaseStatus-Example + - reference: Observation/Observation-GenomicEthnicity-Example + - reference: Observation/Observation-NoPregnancy-Example + - reference: >- + FamilyMemberHistory/FamilyMemberHistory-NonConsanguinousUnion-Example + - reference: Observation/Observation-NoTransplant-Example + - reference: Observation/Observation-NoTransfusion-Example + - reference: Condition/Condition-HearingLoss-Example + note: + - text: No family history of genomic testing + - text: >- + Free text for diagnosis/reason for referral, relevant + information including family history, phenotypic + details/ HPO Terms/Patient in need of test...example + multiple-items: + description: >- + A successful response to a service request get, contains a + multiple items. + value: + resourceType: Bundle + type: searchset + entry: + - resourceType: ServiceRequest + id: ServiceRequest-NonWGSTestOrderForm-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory + code: nhs + display: NHS + status: active + intent: order + category: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory + code: rare-disease-non-wgs + display: Rare Disease - Non-WGS + priority: routine + code: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R67.2 + display: Monogenic hearing loss + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + authoredOn: '2023-08-05' + requester: + reference: PractitionerRole/PractitionerRole-GeneSmithENT-Example + reasonCode: + - coding: + - system: http://snomed.info/sct + code: '103693007' + display: Diagnostic procedure + supportingInfo: + - reference: Observation/Observation-DiseaseStatus-Example + - reference: Observation/Observation-GenomicEthnicity-Example + - reference: Observation/Observation-NoPregnancy-Example + - reference: >- + FamilyMemberHistory/FamilyMemberHistory-NonConsanguinousUnion-Example + - reference: Observation/Observation-NoTransplant-Example + - reference: Observation/Observation-NoTransfusion-Example + - reference: Condition/Condition-HearingLoss-Example + note: + - text: No family history of genomic testing + - text: >- + Free text for diagnosis/reason for referral, relevant + information including family history, phenotypic + details/ HPO Terms/Patient in need of test...example + - resourceType: ServiceRequest + id: ServiceRequest-NonWGSTestOrderForm-FetalScenario-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory + code: nhs + display: NHS + status: active + intent: order + category: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory + code: rare-disease-non-wgs + display: Rare Disease - Non-WGS + priority: urgent + code: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R21 + display: Fetal anomalies with a likely genetic cause + subject: + reference: Patient/Patient-FoetusOfRyanneBoulder-Example + identifier: + - system: urn:oid:2.XX.XXX.X.XXXXXX.X.X.X.X.X.18.24 + value: FT-RWT13521 + assigner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RAX + authoredOn: '2023-09-25' + requester: + reference: >- + PractitionerRole/PractitionerRole-LoisLaneKingstonClinicalGenetics-Example + reasonCode: + - coding: + - system: http://snomed.info/sct + code: '243787009' + display: Antenatal screening + supportingInfo: + - reference: Observation/Observation-HistoryOfFetalLoss-Example + - reference: Observation/Observation-NonConsanguinousUnion-Example + - reference: >- + FamilyMemberHistory/FamilyMemberHistory-NonConsanguinousUnionRyanneBoulder-Example + - reference: Observation/Observation-GenomicEthnicity-Example + - reference: Observation/Observation-PregnancyConfirmation-Example + - reference: Observation/Observation-NoTransplant-Example + - reference: >- + Observation/Observation-NoFirstTrimesterFetalAnomalies-Example + - reference: >- + Observation/Observation-NoSecondTrimesterFetalAnomalies-Example + - reference: Procedure/Procedure-InVitroFertilisation-Example + note: + - text: Samples are to be provided at a later date + - text: No family history of relevant testing + - text: >- + Free text for diagnosis/reason for referral, relevant + information including family history, phenotypic + details/ HPO Terms/ E.g. large echogenic kidneys with + normal bladder + 200-goms-bundle-service-request-read: + description: | + Read Service Request operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A single [FHIR + ServiceRequest](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-ServiceRequest) + examples: + single-item: + description: >- + A successful response to a service request get, contains a + single item. + value: + resourceType: ServiceRequest + id: ServiceRequest-NonWGSTestOrderForm-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory + code: nhs + display: NHS + status: active + intent: order + category: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory + code: rare-disease-non-wgs + display: Rare Disease - Non-WGS + priority: routine + code: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R67.2 + display: Monogenic hearing loss + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + authoredOn: '2023-08-05' + requester: + reference: PractitionerRole/PractitionerRole-GeneSmithENT-Example + reasonCode: + - coding: + - system: http://snomed.info/sct + code: '103693007' + display: Diagnostic procedure + supportingInfo: + - reference: Observation/Observation-DiseaseStatus-Example + - reference: Observation/Observation-GenomicEthnicity-Example + - reference: Observation/Observation-NoPregnancy-Example + - reference: >- + FamilyMemberHistory/FamilyMemberHistory-NonConsanguinousUnion-Example + - reference: Observation/Observation-NoTransplant-Example + - reference: Observation/Observation-NoTransfusion-Example + - reference: Condition/Condition-HearingLoss-Example + note: + - text: No family history of genomic testing + - text: >- + Free text for diagnosis/reason for referral, relevant + information including family history, phenotypic details/ + HPO Terms/Patient in need of test...example + 200-goms-bundle-service-request-history: + description: | + Read Service Request history operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A Bundle containing [FHIR ServiceRequest](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-ServiceRequest) + history + examples: + multiple-items: + description: >- + A successful response to a service request get, contains a + multiple items. + value: + resourceType: Bundle + type: history + entry: + - resourceType: ServiceRequest + id: ServiceRequest-NonWGSTestOrderForm-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory + code: nhs + display: NHS + status: active + intent: order + category: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory + code: rare-disease-non-wgs + display: Rare Disease - Non-WGS + priority: routine + code: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R67.2 + display: Monogenic hearing loss + subject: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + authoredOn: '2023-08-05' + requester: + reference: PractitionerRole/PractitionerRole-GeneSmithENT-Example + reasonCode: + - coding: + - system: http://snomed.info/sct + code: '103693007' + display: Diagnostic procedure + supportingInfo: + - reference: Observation/Observation-DiseaseStatus-Example + - reference: Observation/Observation-GenomicEthnicity-Example + - reference: Observation/Observation-NoPregnancy-Example + - reference: >- + FamilyMemberHistory/FamilyMemberHistory-NonConsanguinousUnion-Example + - reference: Observation/Observation-NoTransplant-Example + - reference: Observation/Observation-NoTransfusion-Example + - reference: Condition/Condition-HearingLoss-Example + note: + - text: No family history of genomic testing + - text: >- + Free text for diagnosis/reason for referral, relevant + information including family history, phenotypic + details/ HPO Terms/Patient in need of test...example + - resourceType: ServiceRequest + id: ServiceRequest-NonWGSTestOrderForm-FetalScenario-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory + code: nhs + display: NHS + status: active + intent: order + category: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory + code: rare-disease-non-wgs + display: Rare Disease - Non-WGS + priority: urgent + code: + coding: + - system: >- + https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory + code: R21 + display: Fetal anomalies with a likely genetic cause + subject: + reference: Patient/Patient-FoetusOfRyanneBoulder-Example + identifier: + - system: urn:oid:2.XX.XXX.X.XXXXXX.X.X.X.X.X.18.24 + value: FT-RWT13521 + assigner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RAX + authoredOn: '2023-09-25' + requester: + reference: >- + PractitionerRole/PractitionerRole-LoisLaneKingstonClinicalGenetics-Example + reasonCode: + - coding: + - system: http://snomed.info/sct + code: '243787009' + display: Antenatal screening + supportingInfo: + - reference: Observation/Observation-HistoryOfFetalLoss-Example + - reference: Observation/Observation-NonConsanguinousUnion-Example + - reference: >- + FamilyMemberHistory/FamilyMemberHistory-NonConsanguinousUnionRyanneBoulder-Example + - reference: Observation/Observation-GenomicEthnicity-Example + - reference: Observation/Observation-PregnancyConfirmation-Example + - reference: Observation/Observation-NoTransplant-Example + - reference: >- + Observation/Observation-NoFirstTrimesterFetalAnomalies-Example + - reference: >- + Observation/Observation-NoSecondTrimesterFetalAnomalies-Example + - reference: Procedure/Procedure-InVitroFertilisation-Example + note: + - text: Samples are to be provided at a later date + - text: No family history of relevant testing + - text: >- + Free text for diagnosis/reason for referral, relevant + information including family history, phenotypic + details/ HPO Terms/ E.g. large echogenic kidneys with + normal bladder + 200-goms-bundle-diagnostic-report-read: + description: | + Read diagnostic report operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A single [FHIR + DiagnosticReport](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-DiagnosticReport) + examples: + single-item: + description: >- + A successful response to a diagnostic report get, contains a + single item. + value: + resourceType: DiagnosticReport + id: DiagnosticReport-AnitaLamberts-Example + identifier: + - system: https://www.guysandstthomas.nhs.uk/SEGLH/lims + value: FHGenomicReport + assigner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RJ1 + basedOn: + - reference: >- + ServiceRequest/ServiceRequest-NonWGSTestOrderForm-NewFollowupTest-Example + status: final + category: + - coding: + - system: http://terminology.hl7.org/CodeSystem/v2-0074 + code: GE + display: Genetics + code: + coding: + - system: http://snomed.info/sct + code: '1054161000000101' + display: Genetic report + subject: + reference: Patient/Patient-AnitaLamberts-Example + issued: '2023-11-24T09:45:00Z' + performer: + - identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RJ1 + specimen: + - reference: Specimen/Specimen-BloodEDTA-Example + presentedForm: + - contentType: application/pdf + language: en-GB + url: https://o719on.axshare.com/?id=8aol33&p=introduction&g=1 + size: 43272 + title: Genomic Report for Anita Lamberts + creation: '2023-11-24' + 200-goms-bundle-task-read: + description: | + Read Task operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A single [FHIR + Task](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Task) + examples: + single-item: + description: A successful response to a task get, contains a single item. + value: + resourceType: Task + id: Task-NonWGSRareDiseaseTestOrder-Example + status: requested + intent: order + priority: routine + code: + coding: + - system: https://fhir.nhs.uk/CodeSystem/task-code-genomics + code: ProcessGenomicTestRequest + display: Process Genomic Test Request + focus: + reference: ServiceRequest/ServiceRequest-SavedTestOrder-Example + for: + reference: Patient/Patient-MeirLieberman-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + authoredOn: '2023-08-05' + requester: + reference: PractitionerRole/PractitionerRole-GeneSmithENT-Example + 20X-goms-bundle-specimen-create-update: + description: A response from the /FHIR/R4/Specimen create update action. + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: > + A FHIR + [Specimen](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-Specimen) + examples: + single-item: + description: Specimen for update + value: + resourceType: Specimen + id: 9e2e2b25-1d24-460d-965e-6b86727eb3b4 + identifier: + - system: https://fhir.leedsth.nhs.uk//Id/specimenId + value: RR8-696B0-17843 + status: available + type: + coding: + - system: http://snomed.info/sct + code: '445295009' + display: Blood specimen with EDTA + subject: + reference: Patient/Patient-FayMutlow-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307806' + collection: + collector: + identifier: + system: https://fhir.nhs.uk/Id/sds-user-id + value: '9999999998' + display: Phletobomist-Lois Lane + collectedDateTime: '2023-10-05T15:30:00Z' + request: + - reference: >- + ServiceRequest/ServiceRequest-SavedTestOrderUpdated-CascadeTesting-Example + 200-goms-bundle-specimen-read: + description: | + Read Specimen operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A single [FHIR + Specimen](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-Specimen) + examples: + single-item: + description: A successful response to a specimen get, contains a single item. + value: + resourceType: Specimen + id: Specimen-PheobeSmitham-Example + identifier: + - system: https://fhir.leedssth.nhs.uk//Id/specimenId + value: RGD-69050-P-RR12764 + status: available + type: + coding: + - system: http://snomed.info/sct + code: '445295009' + display: Blood specimen with EDTA + subject: + reference: Patient/Patient-PheobeSmitham-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307539' + collection: + collector: + identifier: + system: https://fhir.nhs.uk/Id/sds-user-id + value: '9999999998' + display: Phletobomist-Lois Lane + collectedDateTime: '2023-09-17' + request: + - reference: >- + ServiceRequest/ServiceRequest-WGSTestOrderForm-TrioTestingProband-Example + 200-goms-bundle-practitionerrole-get-logical-id: + description: | + Read patient operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A single [FHIR + Patient](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-Patient) + examples: + single-item: + description: A successful response to a patient get, contains a single item. + value: + resourceType: PractitionerRole + id: PractitionerRole-EugeneSmith-Example + practitioner: + identifier: + system: https://fhir.nhs.uk/Id/sds-user-id + value: '9999999998' + display: Dr. Eugene Smith + organization: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RPA02 + display: MEDWAY MARITIME HOSPITAL + specialty: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-PracticeSettingCode + code: '820' + display: General Pathology + telecom: + - system: phone + value: '01634976477' + - system: email + value: medwaypath@nhs.net + - system: email + value: clinicalgeneticsmedway@nhs.net + extension: + - url: >- + http://hl7.org/fhir/StructureDefinition/contactpoint-comment + valueString: reporting + - system: email + value: asmithgppracticeg@nhs.net + extension: + - url: >- + http://hl7.org/fhir/StructureDefinition/contactpoint-comment + valueString: reporting + 200-goms-bundle-practitionerrole-get: + description: | + Read practitioner role operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A FHIR + [bundle](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Bundle) + with collection of [FHIR PractitionerRole](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-PractitionerRole.page.md) + examples: + single-item: + description: A successful response to a patient get, contains a single item. + value: + resourceType: Bundle + type: searchset + entry: + - resourceType: PractitionerRole + id: PractitionerRole-EugeneSmith-Example + practitioner: + identifier: + system: https://fhir.nhs.uk/Id/sds-user-id + value: '9999999998' + display: Dr. Eugene Smith + organization: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RPA02 + display: MEDWAY MARITIME HOSPITAL + specialty: + - coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-PracticeSettingCode + code: '820' + display: General Pathology + telecom: + - system: phone + value: '01634976477' + - system: email + value: medwaypath@nhs.net + - system: email + value: clinicalgeneticsmedway@nhs.net + extension: + - url: >- + http://hl7.org/fhir/StructureDefinition/contactpoint-comment + valueString: reporting + - system: email + value: asmithgppracticeg@nhs.net + extension: + - url: >- + http://hl7.org/fhir/StructureDefinition/contactpoint-comment + valueString: reporting + 200-goms-bundle-relatedperson-get: + description: | + Read related person operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A FHIR + [bundle](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Bundle) + with collection of [FHIR RelatedPerson](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-RelatedPerson.page.md) + examples: + single-item: + description: A successful response to a patient get, contains a single item. + value: + resourceType: Bundle + type: searchset + entry: + - resourceType: RelatedPerson + id: RelatedPerson-AliceSmithamProbandMother-Example + identifier: + system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307246' + patient: + reference: Patient/Patient-PheobeSmitham-Example + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RPA02 + relationship: + - coding: + - system: >- + http://terminology.hl7.org/CodeSystem/v3-RoleCode + code: 'NMTH' + display: natural mother + 200-goms-bundle-patient-get-logical-id: + description: | + Read patient operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A single [FHIR + Patient](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-Patient) + examples: + single-item: + description: A successful response to a patient get, contains a single item. + value: + resourceType: Patient + id: Patient-MeirLieberman-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BirthSex + valueCodeableConcept: + coding: + - system: >- + http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender + code: M + display: Male + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-EthnicCategory + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-EthnicCategoryEngland + code: A + display: White - British + identifier: + - system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-NHSNumberVerificationStatus + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-NHSNumberVerificationStatusEngland + version: 2.2.0 + code: '01' + display: Number present and verified + - system: urn:oid:2.XX.XXX.X.XXXXXX.X.X.X.X.X.18.24 + value: RGT012423 + assigner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RGT01 + - system: https://fhir.nhs.uk/Id/genomics-pedigree-number + value: P12345 + name: + - given: + - Meir + - Anah + family: Lieberman + gender: male + birthDate: '2005-12-19' + deceasedBoolean: false + address: + - line: + - 1 Spinney Close + - Worcester Park + city: Surrey + postalCode: KT4 7BS + generalPractitioner: + - identifier: + system: https://fhir.hl7.org.uk/Id/gmp-number + value: G9999999 + display: Dr. Aero Smith + - identifier: + system: https://fhir.hl7.org.uk/Id/ODS-code + value: TP123 + display: 123 Test Practice + link: + - other: + reference: >- + https://api.service.nhs.uk/personal-demographics/FHIR/R4/Patient/9449307873 + type: seealso + 200-goms-bundle-patient-get: + description: | + Read patient operation successful + content: + application/fhir+json: + schema: + type: object + required: + - resourceType + - identifier + - type + - entry + description: >- + A FHIR + [bundle](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/Bundle) + with collection of [FHIR + Patient](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/Profiles/All-Profiles/UKCore-Patient) + examples: + single-item: + description: A successful response to a patient get, contains a single item. + value: + resourceType: Bundle + type: searchset + entry: + - resourceType: Patient + id: Patient-MeirLieberman-Example + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BirthSex + valueCodeableConcept: + coding: + - system: >- + http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender + code: M + display: Male + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-EthnicCategory + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-EthnicCategoryEngland + code: A + display: White - British + identifier: + - system: https://fhir.nhs.uk/Id/nhs-number + value: '9449307873' + extension: + - url: >- + https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-NHSNumberVerificationStatus + valueCodeableConcept: + coding: + - system: >- + https://fhir.hl7.org.uk/CodeSystem/UKCore-NHSNumberVerificationStatusEngland + version: 2.2.0 + code: '01' + display: Number present and verified + - system: urn:oid:2.XX.XXX.X.XXXXXX.X.X.X.X.X.18.24 + value: RGT012423 + assigner: + identifier: + system: https://fhir.nhs.uk/Id/ods-organization-code + value: RGT01 + - system: https://fhir.nhs.uk/Id/genomics-pedigree-number + value: P12345 + name: + - given: + - Meir + - Anah + family: Lieberman + gender: male + birthDate: '2005-12-19' + deceasedBoolean: false + address: + - line: + - 1 Spinney Close + - Worcester Park + city: Surrey + postalCode: KT4 7BS + generalPractitioner: + - identifier: + system: https://fhir.hl7.org.uk/Id/gmp-number + value: G9999999 + display: Dr. Aero Smith + - identifier: + system: https://fhir.hl7.org.uk/Id/ODS-code + value: TP123 + display: 123 Test Practice + link: + - other: + reference: >- + https://api.service.nhs.uk/personal-demographics/FHIR/R4/Patient/9449307873 + type: seealso + parameters: + CorrelationID: + in: header + name: X-Correlation-ID + required: false + description: > + An optional ID which you can use to track transactions across multiple + systems. It can take any value, but we recommend avoiding `.` + characters. Mirrored back in a response header. + schema: + type: string + pattern: >- + ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$ + example: 60E0B220-8136-4CA5-AE46-1D97EF59D068 + If-Match: + in: header + name: If-Match + required: true + description: > + The version id for the resource updated + schema: + type: string + example: 1 + GetPages: + in: query + name: _getpages + required: false + description: > + Pages identifier + schema: + type: string + pattern: >- + ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$ + example: 60E0B220-8136-4CA5-AE46-1D97EF59D068 + GetPageOffset: + in: query + name: _getpagesoffset + required: false + description: > + Page Offset + schema: + type: string + example: 20 + Count: + in: query + name: _count + required: false + description: > + Page Offset + schema: + type: string + example: 20 + RequestID: + in: header + name: X-Request-ID + required: true + description: > + A optional globally unique identifier (GUID) for the request, which we + use to de-duplicate repeated requests and to trace the request if you + contact our helpdesk. + + Must be a universally unique identifier (UUID) (ideally version 4). + + Mirrored back in a response header. + + If you re-send a failed request, use the same value in this header. + schema: + type: string + pattern: >- + ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$ + example: 60E0B220-8136-4CA5-AE46-1D97EF59D068 + PatientIdentifier: + in: query + name: patient:identifier + description: > + The patient's NHS number. + + Expressed as `|` where `` must be + `https://fhir.nhs.uk/Id/nhs-number` and `` must be a [valid NHS + number](https://www.datadictionary.nhs.uk/attributes/nhs_number.html). + schema: + type: string + example: https://fhir.nhs.uk/Id/nhs-number|9000000009 + Identifier: + in: query + name: identifier + description: | + The resource identifier. + Expressed as `|` + schema: + type: string + example: https://example.org.system|ABCD1234 + PractitionerIdentifier: + in: query + name: practitioner:identifier + description: > + The practitioner identifier within PractitionerRole.practitioner + reference object. + + Expressed as `|` + schema: + type: string + example: https://example.org.system|ABCD1234 + DateFrom: + in: query + name: '-date.from' + description: The earliest date to be included (e.g. 2020-01-01) + schema: + type: string + format: date + default: '1900-01-01' + DateTo: + in: query + name: '-date.to' + description: The latest date to be included (e.g. 2020-12-31) + schema: + type: string + format: date + default: '9999-12-31' + Authored: + in: query + name: authored + description: Search by date request signed - ServiceRequest.authoredOn + schema: + type: string + format: date + default: '1900-01-01' + TaskAuthored: + in: query + name: authored-on + description: Search by creation date - Task.authoredOn + schema: + type: string + format: date + default: '1900-01-01' + ReportIssued: + in: query + name: issued + description: When the report was issued - DiagnosticReport.issued + schema: + type: string + format: date + default: '1900-01-01' + BasedOn: + in: query + name: based-on + description: The service request reference the report related to + schema: + type: string + example: b4dccd9f-1f49-45aa-8566-3a517fc98d3d + SpecimenCollected: + in: query + name: collected + description: The date the specimen was collected Specimen.collection.collected + schema: + type: string + format: date + default: '1900-01-01' + ContainerIdentifier: + in: query + name: container-id + description: >- + Search based on the unique identifier associated with the specimen + container - Specimen.container.identifier + schema: + type: string + example: b4dccd9f-1f49-45aa-8566-3a517fc98d3d + LogicalIdentifier: + in: query + name: _id + description: The logical identifier of the resource + schema: + type: string + example: b4dccd9f-1f49-45aa-8566-3a517fc98d3d + Include: + in: query + name: _include + description: >- + The parameter _include is used to follow links 'forward'. For example, + `ServiceRequest:patient`, will include patient demographic details + referenced within the ServiceRequest. + schema: + type: string + default: null + Graph: + in: query + name: graph + description: >- + The parameter to get all information related to a service request based + on it logical identifier and associated [graph + definition](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/GraphDefinitions) + on server. + schema: + type: string + default: genomics-test-order + GraphRequestGroup: + in: query + name: graph + description: >- + The parameter to get all information related to a service request based + on it logical identifier and associated [graph + definition](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/GraphDefinitions) + on server. + schema: + type: string + default: genomics-trio-test-order + GraphRequestGroupResult: + in: query + name: graph + description: >- + The parameter to get all information related to a service request based + on it logical identifier and associated [graph + definition](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/GraphDefinitions) + on server. + schema: + type: string + default: genomics-trio-result-grouping + GraphReport: + in: query + name: graph + description: >- + The parameter to get all information related to a service request based + on it logical identifier and associated [graph + definition](https://simplifier.net/guide/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/GraphDefinitions) + on server. + schema: + type: string + default: genomics-test-result + TaskInclude: + in: query + name: _include + description: >- + The parameter _include is used to follow links 'forward'. For example, + `Task:owner`, will include Organisation details of the owning the task. + schema: + type: string + default: null + SpecimenInclude: + in: query + name: _include + description: >- + The parameter _include is used to follow links 'forward'. For example, + `Specimen:request`, will include ServiceRequest details managing the + Specimen. + schema: + type: string + default: null + SpecimenRevInclude: + in: query + name: _revinclude + description: >- + The parameter _revinclude is used to follow reverse links. For example. + 'Task:input' will include all tasks managing the specimen workflows. + schema: + type: string + default: null + SpecimenRequest: + in: query + name: request + description: The parameter search specimen based on service request logical id. + schema: + type: string + default: null + DiagnosticReportInclude: + in: query + name: _include + description: >- + The parameter _include is used to follow links 'forward'. + `DiagnosticReport:patient`, will include patient demographic details + referenced within the DiagnosticReport. + schema: + type: string + default: null + RevInclude: + in: query + name: _revinclude + description: >- + The parameter _revinclude is used to follow reverse links. For example + `Task:focus`, will include Tasks that references the ServiceRequest + through focus attributes. + schema: + type: string + default: null + TaskRevInclude: + in: query + name: _revinclude + description: >- + The parameter _revinclude is used to follow reverse links. For example + `Task:focus`, will include Tasks that references the ServiceRequest + through focus attributes. + schema: + type: string + default: null + Requestor: + in: query + name: requester + description: Parameter to search based on requesting Organisation + schema: + type: string + default: null + Performer: + in: query + name: performer + description: Parameter to search based on performing Organisation + schema: + type: string + default: null + ResultsInterpreter: + in: query + name: results-interpreter + description: Parameter to search based on ResultsInterpreter Organisation + schema: + type: string + default: null + Owner: + in: query + name: owner + description: Parameter to search based on owning Organisation + schema: + type: string + default: null + Status: + in: query + name: status + description: Parameter to search based on Status of a Resource + schema: + type: string + default: null + Organisation: + in: query + name: organization:identifier + description: Parameter to search based on organisation code + schema: + type: string + default: null + GivenName: + in: query + name: given + description: Parameter to search based on GivenName of a Patient + schema: + type: string + default: null + FamilyName: + in: query + name: family + description: Parameter to search based on FamilyName of a Patient + schema: + type: string + default: null + DateOfBirth: + in: query + name: birthdate + description: Parameter to search based on DateOfBirth of a Patient + schema: + type: string + format: date + default: '9999-12-31' + Gender: + in: query + name: gender + description: Parameter to search based on Gender of a Patient + schema: + type: string + default: null + TestID: + in: query + name: code + description: >- + Parameter to search Service Request based on [test directory + code](https://www.england.nhs.uk/publication/national-genomic-test-directories/) + schema: + type: string + default: null + Category: + in: query + name: category + description: >- + Parameter to search Service Request based on + [category](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/ValueSets#Genomic-Test-Types) + schema: + type: string + default: null + SupportingInfo: + in: query + name: supporting-info + description: Parameter to search Service Request based on supporting info in the test + schema: + type: string + default: null + BusinessStatus: + in: query + name: business-status + description: >- + Parameter to search based on + [BusinessStatus](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/ValueSets#Genomic-Business-Status) + of a Task Resource + schema: + type: string + default: null + TaskCode: + in: query + name: code + description: >- + Parameter to search based on + [TaskCode](https://simplifier.net/guide/fhir-genomics-implementation-guide/Home/FHIRAssets/CodeSystems#Genomic-Task-Code) + of a Task Resource + schema: + type: string + default: null + NHSDSessionURID: + in: header + name: NHSD-Session-URID + description: > + The user role ID (URID) for the current session. Also known as a user + role profile ID (URPID). + + If you are using User-restricted RESTful APIs - NHS login separate + authentication and authorisation, see [determine the user's + role](https://digital.nhs.uk/developer/guides-and-documentation/security-and-authorisation/user-restricted-restful-apis-nhs-cis2-separate-authentication-and-authorisation#step-9-determine-the-user-s-role) + for guidance. This field is optional. + required: false + schema: + type: string + pattern: ^[0-9]+$ + example: '555254240100' + apikey: + in: header + name: apikey + description: > + An [apikey based on + ](https://digital.nhs.uk/developer/guides-and-documentation/security-and-authorisation/application-restricted-restful-apis-api-key-authentication) + application restricted restful apis. + required: true + schema: + type: string + format: ^apikey\ [[:ascii:]]+$ + example: 58d6862a-61aa-4bdb-9361-392fe4a00dd4 + Authorization: + in: header + name: Authorization + description: > + An [OAuth 2.0 bearer + token](https://digital.nhs.uk/developer/guides-and-documentation/security-and-authorisation#user-restricted-apis). + Required in all environments except sandbox. + required: true + schema: + type: string + format: ^Bearer\ [[:ascii:]]+$ + example: Bearer g1112R_ccQ1Ebbb4gtHBP1aaaNM + Id: + in: path + name: id + required: true + description: | + A required ID which you can use to identify an unique resource object. + Mirrored back in a response header. + schema: + type: string + example: 29dc4e84-7e72-11ee-b962-0242ac120002 + VersionId: + in: path + name: versionId + required: true + description: >- + The specific version Id which you can use to identify an unique resource + object with its logical Id. + schema: + type: string + example: '1' + ResourceName: + in: path + name: resourceName + required: true + description: The specific resource type + schema: + type: string + enum: + - ServiceRequest + - Specimen + - DiagnosticReport + - Task + - PractitionerRole + - Patient + - DocumentReference + - RelatedPerson + - RequestGroup + - Consent + - Condition + - Observation + - QuestionnaireResponse + - Procedure + - BodyStructure + - FamilyMemberHistory + - Provenance + - Group + example: ServiceRequest + schemas: {} + requestBodies: {} + headers: + Location: + schema: + type: string + example: 29dc4e84-7e72-11ee-b962-0242ac120002 + description: The location of the resource. +x-nhsd-apim: + monitoring: true + temporary: false + target: + type: external + healthcheck: /_status + url: https://glu-api.aireinnovate.com/genomics-stag + security: + type: apikey + header: X-Api-Key + secret: order-management-service-dev-api-key + access: + - title: Application Restricted + grants: + app-level0: [] + app-level3: [] + - title: User Restricted + grants: + nhs-cis2-aal3: [] + ratelimiting: + proxy: + limit: 100 + timeunit: minute + app-default: + limit: 200 + timeunit: minute \ No newline at end of file diff --git a/specification/enviroment/beta/genomic-order-management-service-api-specification-beta-int.yaml b/specification/enviroment/beta/genomic-order-management-service-api-specification-beta-int.yaml index 756b8d9..86bd5b9 100644 --- a/specification/enviroment/beta/genomic-order-management-service-api-specification-beta-int.yaml +++ b/specification/enviroment/beta/genomic-order-management-service-api-specification-beta-int.yaml @@ -1,7 +1,7 @@ openapi: 3.0.3 info: title: Genomic Order Management Service (FHIR) API - version: v0.5.2 Beta + version: v0.5.3 Beta description: > ## Overview @@ -446,6 +446,8 @@ x-spec-publication: - method: GET path: /FHIR/R4/PractitionerRole servers: + - url: https://dev.api.service.nhs.uk/genomic-order-management-service + description: Development - url: https://int.api.service.nhs.uk/genomic-order-management-service description: Integration test - url: https://api.service.nhs.uk/genomic-order-management-service @@ -466,6 +468,7 @@ paths: post: operationId: processgenomicrequests security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Process genomic test request @@ -1756,6 +1759,7 @@ paths: get: operationId: getSearchPages security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Get results pages @@ -1781,6 +1785,7 @@ paths: get: operationId: getServiceRequests security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Search for ServiceRequests @@ -1818,6 +1823,10 @@ paths: /FHIR/R4/ServiceRequest/{id}/$graph: get: operationId: getservicerequestinformation + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] summary: Get detailed information around a service request. description: > This endpoint allows to retrieve all related records of a ServiceRequest @@ -1843,6 +1852,7 @@ paths: get: operationId: getRequestGroup security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Search for RequestGroup @@ -1871,6 +1881,10 @@ paths: /FHIR/R4/RequestGroup/{id}/$graph: get: operationId: getrequestgroupinformation + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] summary: Get detailed information around a Request Group. description: > This endpoint allows to retrieve all related records of a ServiceRequest @@ -1896,6 +1910,7 @@ paths: get: operationId: getTasks security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Search for Tasks @@ -1929,6 +1944,7 @@ paths: get: operationId: getDiagnosticReports security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Search for DiagnosticReports @@ -1964,6 +1980,7 @@ paths: get: operationId: getdiagnosticreportinformation security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Get detailed information around a diagnostic report. @@ -1991,6 +2008,7 @@ paths: get: operationId: getSpecimens security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Search for Specimens @@ -2024,6 +2042,7 @@ paths: get: operationId: getPatient security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Search for Patient @@ -2051,6 +2070,7 @@ paths: get: operationId: getRelatedPerson security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Search for RelatedPerson @@ -2079,6 +2099,7 @@ paths: get: operationId: getPractitionerRole security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Search for PractitionerRole @@ -2107,6 +2128,7 @@ paths: post: operationId: validategenomicrequests security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Validate genomic test requests resource without processing them for storage @@ -2132,6 +2154,7 @@ paths: get: operationId: readResource security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Search for resource by its logical id @@ -2159,6 +2182,10 @@ paths: get: summary: Retrieve resource history by its logical id operationId: readResourceHistory + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] description: > ## Overview @@ -2203,6 +2230,10 @@ paths: get: summary: Retrieve Resource version by its logical id operationId: readResourceHistoryVersion + security: + - app-level0: [] + - app-level3: [] + - nhs-cis2-aal3: [] description: > ## Overview @@ -2248,6 +2279,7 @@ paths: get: operationId: readMetadata security: + - app-level0: [] - app-level3: [] - nhs-cis2-aal3: [] summary: Get the capability statement from server @@ -2263,6 +2295,16 @@ paths: '200': description : 'Successful retrieval of metadata.' components: + securitySchemes: + app-level0: + $ref: >- + https://proxygen.prod.api.platform.nhs.uk/components/securitySchemes/app-level0 + app-level3: + $ref: >- + https://proxygen.prod.api.platform.nhs.uk/components/securitySchemes/app-level3 + nhs-cis2-aal3: + $ref: >- + https://proxygen.ptl.api.platform.nhs.uk/components/securitySchemes/nhs-cis2-aal3 responses: 4XX-goms-error: description: > @@ -4733,14 +4775,15 @@ x-nhsd-apim: target: type: external healthcheck: /_status - url: TBC + url: https://glu-api.aireinnovate.com/genomics-stag security: type: apikey header: X-Api-Key - secret: TBC + secret: order-management-service-int-api-key access: - title: Application Restricted grants: + app-level0: [] app-level3: [] - title: User Restricted grants: