From 2e8d12d5a4762a57f0abea33723f41e9797fb668 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Tue, 14 May 2024 15:04:24 +0100 Subject: [PATCH 01/21] Test for strict validation on Genomics --- options.json | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 options.json diff --git a/options.json b/options.json new file mode 100644 index 00000000..3f74d42c --- /dev/null +++ b/options.json @@ -0,0 +1,6 @@ +{ + "strict-validation": true, + "ignore-folders": [], + "ignore-files": [], + "error-if-metaProfile-present": true +} \ No newline at end of file From a2844b4166dfe5d3d24518a9ecd5006dfb781b85 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Wed, 15 May 2024 21:03:28 +0100 Subject: [PATCH 02/21] Structured Reporting 2 Observations, Procedure and Task --- ...vation-GenomicImplication-Therapeutic.json | 98 +++++++++ .../Observation-GenomicsVariant-SLC52A2.json | 190 ++++++++++++++++++ ...Procedure-GenomicsReport-GenomicStudy.json | 33 +++ ...enomicReport-MedicationRecommendation.json | 27 +++ 4 files changed, 348 insertions(+) create mode 100644 Observation/Observation-GenomicImplication-Therapeutic.json create mode 100644 Observation/Observation-GenomicsVariant-SLC52A2.json create mode 100644 Procedure/Procedure-GenomicsReport-GenomicStudy.json create mode 100644 Task/Task-GenomicReport-MedicationRecommendation.json diff --git a/Observation/Observation-GenomicImplication-Therapeutic.json b/Observation/Observation-GenomicImplication-Therapeutic.json new file mode 100644 index 00000000..57fbd04d --- /dev/null +++ b/Observation/Observation-GenomicImplication-Therapeutic.json @@ -0,0 +1,98 @@ +{ + "resourceType": "Observation", + "id": "Observation-GenomicImplication-Therapeutic", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + }, + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0074", + "code": "GE" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example" + }, + "effectiveDateTime": "2023-09-16", + "performer": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "R0A" + } + } + ], + "derivedFrom": [ + { + "reference": "Observation/Oservation-GenomicsVariant-SLC52A2" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication", + "display": "Therapeutic Implication" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6677-4", + "display": "Responsive" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51963-7", + "display": "Medication assessed" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "9346", + "display": "riboflavin" + } + ] + } + } + ], + "note" : [{ + "text" : "High dose riboflavin supplementation has been reported to ameliorate the progression of this disorder (Foley et al 2014 PMID22740598)" + }] +} \ No newline at end of file diff --git a/Observation/Observation-GenomicsVariant-SLC52A2.json b/Observation/Observation-GenomicsVariant-SLC52A2.json new file mode 100644 index 00000000..4a97895f --- /dev/null +++ b/Observation/Observation-GenomicsVariant-SLC52A2.json @@ -0,0 +1,190 @@ +{ + "resourceType": "Observation", + "id": "Observation-GenomicsVariant-SLC52A2", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "status": "final", + "basedOn": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + } + ], + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + }, + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0074", + "code": "GE" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "69548-6" + }, + { + "system": "http://snomed.info/sct", + "code": "699866005", + "display": "Brown-Vialetto-Van Laere syndrome" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example" + }, + "effectiveDateTime": "2023-09-16", + "performer": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "R0A" + } + } + ], + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA9633-4", + "display": "Present" + } + ] + }, + "method": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA26398-0", + "display": "Sequencing" + } + ] + }, + "specimen": { + "reference": "Specimen/Specimen-PheobeSmitham-Example" + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48018-6" + } + ], + "text": "SLC52A2" + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.genenames.org", + "code": "HGNC:30224", + "display": "SLC52A2" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53034-5" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6705-3", + "display": "homozygous" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "94186-4" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA4489-6", + "display": "Unknown" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81290-9" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://varnomen.hgvs.org", + "code": "NM_001363118.2:c.916G>A" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48001-2" + } + ] + }, + "valueCodeableConcept": { + "text": "Biallelic Pathogenic:SLC52A2 missense variant" + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48002-0" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6683-2", + "display": "Germline" + } + ], + "text": "Pathogenic" + } + } + ] +} \ No newline at end of file diff --git a/Procedure/Procedure-GenomicsReport-GenomicStudy.json b/Procedure/Procedure-GenomicsReport-GenomicStudy.json new file mode 100644 index 00000000..11586e65 --- /dev/null +++ b/Procedure/Procedure-GenomicsReport-GenomicStudy.json @@ -0,0 +1,33 @@ +{ + "resourceType" : "Procedure", + "id" : "Procedure-GenomicsReport-GenomicStudy", + "meta" : { + "profile" : ["http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study"] + }, + "basedOn" : [{ + "reference" : "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + }], + "status" : "completed", + "category" : { + "coding" : [{ + "system" : "http://terminology.hl7.org/CodeSystem/observation-category", + "code" : "laboratory" + }] + }, + "code" : { + "coding" : [ + { + "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs", + "code" : "struc-var", + "display" : "Structural variation detection" + } + ] + }, + "subject" : { + "reference" : "Patient/Patient-PheobeSmitham-Example" + }, + "performedDateTime" : "2023-09-16", + "note" : [{ + "text" : "Proband whole genome sequencing by the 100,000 Genomics Project with analysis of the PanelApp Paediatric motor neuronopathies (version 1.6) gene panel followed by in-house Sanger sequencing confirmation. Please note that the sensitivity of this test is limited by the types of detectable pathogenic variants, regions of low read depth coverage and incomplete ascertainment of disease-gene associations. Further information including read depth coverage is available on request. *Variants are classified using the ACMG/AMP guidelines (Richards et al 2015 PMID25741868)." + }] +} \ No newline at end of file diff --git a/Task/Task-GenomicReport-MedicationRecommendation.json b/Task/Task-GenomicReport-MedicationRecommendation.json new file mode 100644 index 00000000..9531418e --- /dev/null +++ b/Task/Task-GenomicReport-MedicationRecommendation.json @@ -0,0 +1,27 @@ +{ + "resourceType" : "Task", + "id" : "Task-GenomicReport-MedicationRecommendation", + "meta" : { + "profile" : [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation" + ] + }, + "status" : "requested", + "intent" : "proposal", + "code" : { + "coding" : [ + { + "system" : "http://loinc.org", + "code" : "LA14021-2", + "display" : "Confirmatory testing recommended" + } + ] + }, + "description" : "Testing of Pheobe's parents is recommended (via referral to the clinical genetics service) in order to confirm that both are heterozygous carriers of the missense variant.", + "for" : { + "reference" : "Patient/Patient-PheobeSmitham-Example" + }, + "reasonReference" : { + "reference" : "Observation/Observation-GenomicImplication-Therapeutic" + } +} \ No newline at end of file From 810aec569ec1db06e3fa3657f61c32ebbc4e987f Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Thu, 16 May 2024 09:18:23 +0100 Subject: [PATCH 03/21] Adding GenomicReporting IG to dependencies Additional updates to support strict validation --- ...al-FamilyMemberHistory-Genomics.StructureDefinition.json | 2 +- .../NHSDigital-Procedure-Genomics.StructureDefinition.json | 4 ++-- fhirpkg.lock.json | 6 ++++-- options.json | 2 +- package.json | 3 ++- 5 files changed, 10 insertions(+), 7 deletions(-) diff --git a/StructureDefinition/NHSDigital-FamilyMemberHistory-Genomics.StructureDefinition.json b/StructureDefinition/NHSDigital-FamilyMemberHistory-Genomics.StructureDefinition.json index d1a55273..af54b540 100644 --- a/StructureDefinition/NHSDigital-FamilyMemberHistory-Genomics.StructureDefinition.json +++ b/StructureDefinition/NHSDigital-FamilyMemberHistory-Genomics.StructureDefinition.json @@ -50,7 +50,7 @@ "targetProfile": [ "https://fhir.hl7.org.uk/StructureDefinition/UKCore-AllergyIntolerance", "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse", - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DocumentReference", + "http://hl7.org/fhir/StructureDefinition/DocumentReference", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Condition-Genomics", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Observation-Genomics", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-DiagnosticReport-Genomics" diff --git a/StructureDefinition/NHSDigital-Procedure-Genomics.StructureDefinition.json b/StructureDefinition/NHSDigital-Procedure-Genomics.StructureDefinition.json index 9053ca40..359188e2 100644 --- a/StructureDefinition/NHSDigital-Procedure-Genomics.StructureDefinition.json +++ b/StructureDefinition/NHSDigital-Procedure-Genomics.StructureDefinition.json @@ -141,7 +141,7 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DocumentReference", + "http://hl7.org/fhir/StructureDefinition/DocumentReference", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Condition-Genomics", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-DiagnosticReport-Genomics", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Observation-Genomics", @@ -158,7 +158,7 @@ "code": "Reference", "targetProfile": [ "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Composition", - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DocumentReference", + "http://hl7.org/fhir/StructureDefinition/DocumentReference", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-DiagnosticReport-Genomics" ], "aggregation": [ diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 829d2cb0..2b8ad7b1 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,8 +1,10 @@ { - "updated": "2023-09-18T12:13:04.1481382+01:00", + "updated": "2024-05-16T09:14:29.5276199+01:00", "dependencies": { "fhir.r4.ukcore.stu2": "2.0.0", "hl7.fhir.r4.core": "4.0.1" }, - "missing": {} + "missing": { + "hl7.fhir.uv.genomics-reporting": "3.0.1-SNAPSHOT" + } } diff --git a/options.json b/options.json index 3f74d42c..ac6548a1 100644 --- a/options.json +++ b/options.json @@ -2,5 +2,5 @@ "strict-validation": true, "ignore-folders": [], "ignore-files": [], - "error-if-metaProfile-present": true + "error-if-metaProfile-present": false } \ No newline at end of file diff --git a/package.json b/package.json index a73cebf3..475d5531 100644 --- a/package.json +++ b/package.json @@ -8,6 +8,7 @@ "jurisdiction": "urn:iso:std:iso:3166:-2:GB-ENG", "dependencies": { "fhir.r4.ukcore.stu2": "2.0.0", - "hl7.fhir.r4.core": "4.0.1" + "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.uv.genomics-reporting": "3.0.1-SNAPSHOT" } } From 2081c050d4d5add9f4a9ba7c372e3a32722bbb9b Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Thu, 16 May 2024 10:02:30 +0100 Subject: [PATCH 04/21] Addition of UV Genomic Reporting profiles to CS (Capability Statement) --- ...abilityStatement-genomics-application.json | 3724 +++++++++-------- fhirpkg.lock.json | 4 +- 2 files changed, 1959 insertions(+), 1769 deletions(-) diff --git a/CapabilityStatement/CapabilityStatement-genomics-application.json b/CapabilityStatement/CapabilityStatement-genomics-application.json index 4fcc5d60..23429ad0 100644 --- a/CapabilityStatement/CapabilityStatement-genomics-application.json +++ b/CapabilityStatement/CapabilityStatement-genomics-application.json @@ -1,1769 +1,1959 @@ { - "resourceType": "CapabilityStatement", - "id": "CapabilityStatement-genomics-application", - "url": "https://fhir.nhs.uk/CapabilityStatement/CapabilityStatement-genomics-application", - "version": "0.1.0", - "name": "CapabilityStatementGenomicsApplication", - "status": "draft", - "date": "2023-02-27T00:00:00+00:00", - "publisher": "NHS England", - "description": "Sample server capability for the Genomic Medicine Service", - "kind": "instance", - "implementationGuide": [ - "https://simplifier.net/guide/fhir-genomics-implementation-guide", - "https://simplifier.net/guide/nhsdigital" - ], - "fhirVersion": "4.0.1", - "format": [ - "application/fhir+json" - ], - "implementation": { - "description": "Exemplar CapabilityStatement for the GMS central broker implementation" - }, - "messaging": [ - { - "endpoint": [ - { - "protocol": { - "system": "http://terminology.hl7.org/CodeSystem/message-transport", - "code": "http", - "display": "HTTP" - }, - "address": "https://[baseUrl]/$process-message" - } - ], - "documentation": "Endpoint which accepts test order and result message bundles. The server saves the whole message as well as splitting the message into its individual resources for ease of updating through RESTful interactions", - "supportedMessage": [ - { - "mode": "receiver", - "definition": "https://fhir.nhs.uk/MessageDefinition/genomic-test-request" - }, - { - "mode": "receiver", - "definition": "https://fhir.nhs.uk/MessageDefinition/genomic-test-response" - } - ] - } - ], - "rest": [ - { - "mode": "server", - "documentation": "RESTful endpoints supported by the Genomic Medicine Service", - "security": { - "service": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/restful-security-service", - "code": "OAuth", - "display": "OAuth2 Token" - } - ] - } - ] - }, - "resource": [ - { - "type": "AuditEvent", - "profile": "http://hl7.org/fhir/StructureDefinition/AuditEvent", - "documentation": "For searching recorded AuditEvents", - "interaction": [ - { - "code": "read" - }, - { - "code": "search-type" - } - ], - "searchParam": [ - { - "name": "action", - "type": "token" - }, - { - "name": "agent", - "type": "reference" - }, - { - "name": "date", - "type": "date" - }, - { - "name": "entity", - "type": "reference" - }, - { - "name": "outcome", - "type": "token" - }, - { - "name": "patient", - "type": "reference" - } - ] - }, - { - "type": "Bundle", - "profile": "http://hl7.org/fhir/StructureDefinition/Bundle", - "documentation": "For posting FHIR transaction bundles (http://hl7.org/fhir/R4B/http.html#transaction) to the server.", - "interaction": [ - { - "code": "create", - "documentation": "Bundle containing ServiceRequest and all supporting resources (Patient, PractitionerRole, Specimen, etc.)" - } - ], - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ] - }, - { - "type": "CodeSystem", - "profile": "http://hl7.org/fhir/StructureDefinition/CodeSystem", - "documentation": "For searching supported CodeSystems", - "interaction": [ - { - "code": "read" - }, - { - "code": "search-type" - } - ], - "searchParam": [ - { - "name": "code", - "type": "token" - }, - { - "name": "context", - "type": "token" - }, - { - "name": "description", - "type": "string" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "name", - "type": "string" - }, - { - "name": "system", - "type": "uri" - }, - { - "name": "title", - "type": "string" - } - ] - }, - { - "type": "ConceptMap", - "profile": "http://hl7.org/fhir/StructureDefinition/ConceptMap", - "documentation": "For searching provided ConceptMaps", - "interaction": [ - { - "code": "read" - }, - { - "code": "search-type" - } - ], - "searchParam": [ - { - "name": "context", - "type": "token" - }, - { - "name": "description", - "type": "string" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "name", - "type": "string" - }, - { - "name": "source-system", - "type": "uri" - }, - { - "name": "target-system", - "type": "uri" - }, - { - "name": "title", - "type": "string" - } - ] - }, - { - "type": "HealthcareService", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-HealthcareService", - "documentation": "Endpoints for interacting with HealthcareService resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "coverage-area", - "type": "reference" - }, - { - "name": "endpoint", - "type": "reference" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "name", - "type": "string" - }, - { - "name": "location", - "type": "reference" - }, - { - "name": "organization", - "type": "reference" - }, - { - "name": "service-category", - "type": "token" - }, - { - "name": "service-type", - "type": "token" - }, - { - "name": "specialty", - "type": "token" - } - ] - }, - { - "type": "MessageDefinition", - "profile": "http://hl7.org/fhir/StructureDefinition/MessageDefinition", - "documentation": "For searching supported MessageDefinitions", - "interaction": [ - { - "code": "read" - }, - { - "code": "search-type" - } - ], - "searchParam": [ - { - "name": "description", - "type": "string" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "name", - "type": "string" - }, - { - "name": "focus", - "type": "token" - }, - { - "name": "title", - "type": "string" - } - ] - }, - { - "type": "NamingSystem", - "profile": "http://hl7.org/fhir/StructureDefinition/NamingSystem", - "documentation": "For searching supported NamingSystems", - "interaction": [ - { - "code": "read" - }, - { - "code": "search-type" - } - ], - "searchParam": [ - { - "name": "context", - "type": "token" - }, - { - "name": "description", - "type": "string" - }, - { - "name": "name", - "type": "string" - } - ] - }, - { - "type": "Parameters", - "profile": "http://hl7.org/fhir/StructureDefinition/Parameters" - }, - { - "type": "StructureMap", - "profile": "http://hl7.org/fhir/StructureDefinition/StructureMap", - "documentation": "For searching provided StructureMaps", - "interaction": [ - { - "code": "read" - }, - { - "code": "search-type" - } - ], - "searchParam": [ - { - "name": "context", - "type": "token" - }, - { - "name": "description", - "type": "string" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "name", - "type": "string" - } - ] - }, - { - "type": "ValueSet", - "profile": "http://hl7.org/fhir/StructureDefinition/ValueSet", - "documentation": "For searching supported CodeSystems", - "interaction": [ - { - "code": "read" - }, - { - "code": "search-type" - } - ], - "searchParam": [ - { - "name": "code", - "type": "token" - }, - { - "name": "context", - "type": "token" - }, - { - "name": "description", - "type": "string" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "name", - "type": "string" - }, - { - "name": "title", - "type": "string" - } - ] - }, - { - "type": "MessageHeader", - "profile": "http://hl7.org/fhir/StructureDefinition/MessageHeader", - "documentation": "Endpoints for interacting with MessageHeader resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "no-version", - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "code", - "type": "token" - }, - { - "name": "destination", - "type": "string" - }, - { - "name": "destination-uri", - "type": "uri" - }, - { - "name": "focus", - "type": "reference" - }, - { - "name": "sender", - "type": "reference" - }, - { - "name": "source", - "type": "string" - }, - { - "name": "source-uri", - "type": "uri" - } - ] - }, - { - "type": "Subscription", - "profile": "http://hl7.org/fhir/StructureDefinition/Subscription", - "documentation": "Endpoints for interacting with Subscription resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "searchParam": [ - { - "name": "contact", - "type": "token" - }, - { - "name": "criteria", - "type": "string" - }, - { - "name": "status", - "type": "token" - }, - { - "name": "type", - "type": "token" - }, - { - "name": "url", - "type": "uri" - } - ] - }, - { - "type": "CapabilityStatement", - "profile": "http://hl7.org/fhir/StructureDefinition/CapabilityStatement", - "documentation": "For searching provided CapabilityStatements", - "interaction": [ - { - "code": "read" - }, - { - "code": "search-type" - } - ], - "searchParam": [ - { - "name": "description", - "type": "string" - }, - { - "name": "format", - "type": "token" - }, - { - "name": "mode", - "type": "token" - }, - { - "name": "name", - "type": "string" - }, - { - "name": "resource", - "type": "token" - }, - { - "name": "resource-profile", - "type": "reference" - }, - { - "name": "title", - "type": "string" - } - ] - }, - { - "type": "Task", - "profile": "http://hl7.org/fhir/StructureDefinition/Task", - "documentation": "Endpoints for interacting with Task resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update", - "documentation": "Allow an organisation to claim or update a task. If pro-active notification is implemented GEL, GLH and LGL would also need to implement this endpoint to receive updates to their tasks, including cancellation/retraction of requests." - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create", - "documentation": "New tasks are created as the test request is submitted. Connected systems passing on the request may need to create a new task and may need to store new associated resources, in which case a Transaction Bundle should be used. In the IG, it is proposed that POST Task can be used to notify a service of a task, but this assumes that any referenced resources exist, which would need to be retrieved individually. If pro-active notification of Tasks is required the GLH, GEL and LGL should implement the FHIR transaction interaction, but this is out of scope for the Alpha." - }, - { - "code": "search-type", - "documentation": "Allows an organisation to search for tasks. Allows an organisation to find out the current state of the tasks associated with a service request. All search parameters listed should be supported. For polling, a consumer might want to be able to search for all tasks assigned to them, or by other attributes." - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "based-on", - "type": "reference" - }, - { - "name": "business-status", - "type": "token" - }, - { - "name": "code", - "type": "token" - }, - { - "name": "focus", - "type": "reference" - }, - { - "name": "modified", - "type": "date" - }, - { - "name": "owner", - "type": "reference" - }, - { - "name": "subject", - "type": "reference" - }, - { - "name": "performer", - "type": "token" - }, - { - "name": "period", - "type": "date" - }, - { - "name": "priority", - "type": "token" - }, - { - "name": "requester", - "type": "reference" - }, - { - "name": "status", - "type": "token" - } - ] - }, - { - "type": "ServiceRequest", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-ServiceRequest", - "documentation": "Endpoints for interacting with ServiceRequest resources.", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update", - "documentation": "Used to update the ServiceRequest resource, e.g. for adding a specimen reference or updating the status to completed." - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type", - "documentation": "EHR may poll for updates to ServiceRequest or a user might be looking for historical test requests and DiagnosticReports, which would require them to be searchable. For organisations in the chain fulfilling the service request they might want to query service requests for information." - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "authored", - "type": "date" - }, - { - "name": "based-on", - "type": "reference" - }, - { - "name": "category", - "type": "token" - }, - { - "name": "code", - "type": "token" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "intent", - "type": "token" - }, - { - "name": "subject", - "type": "reference" - }, - { - "name": "performer", - "type": "reference" - }, - { - "name": "performer-type", - "type": "token" - }, - { - "name": "priority", - "type": "token" - }, - { - "name": "replaces", - "type": "reference" - }, - { - "name": "requester", - "type": "reference" - }, - { - "name": "specimen", - "type": "reference" - }, - { - "name": "status", - "type": "token" - }, - { - "name": "supporting-info", - "type": "reference" - } - ] - }, - { - "type": "PractitionerRole", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-PractitionerRole", - "documentation": "Endpoints for interacting with PractitionerRole resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "endpoint", - "type": "reference" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "organization", - "type": "reference" - }, - { - "name": "practitioner", - "type": "reference" - }, - { - "name": "specialty", - "type": "token" - }, - { - "name": "telecom", - "type": "token" - } - ] - }, - { - "type": "Practitioner", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Practitioner", - "documentation": "Endpoints for interacting with Practitioner resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "name", - "type": "string" - }, - { - "name": "identifier", - "type": "token" - } - ] - }, - { - "type": "Organization", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization", - "documentation": "Endpoints for interacting with PractitionerRole resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "address", - "type": "string" - }, - { - "name": "endpoint", - "type": "reference" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "name", - "type": "string" - }, - { - "name": "partof", - "type": "reference" - }, - { - "name": "type", - "type": "token" - } - ] - }, - { - "type": "DiagnosticReport", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport", - "documentation": "Endpoints for interacting with DiagnosticReport resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update", - "documentation": "Allows a DiagnosticReport to be updated. Could also be used to notify requesters that a DiagnosticReport has been updated, if proactive notification is implemented." - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create", - "documentation": "Allows a DiagnosticReport to be created on the service. Triggers notification to the requester that a DiagnosticReport is available." - }, - { - "code": "search-type", - "documentation": "Not required for alpha build, but could be used to retrieve historical diagnostic reports." - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "based-on", - "type": "reference" - }, - { - "name": "category", - "type": "token" - }, - { - "name": "code", - "type": "token" - }, - { - "name": "conclusion", - "type": "token" - }, - { - "name": "date", - "type": "date" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "issued", - "type": "date" - }, - { - "name": "subject", - "type": "reference" - }, - { - "name": "performer", - "type": "reference" - }, - { - "name": "result", - "type": "reference" - }, - { - "name": "results-interpreter", - "type": "reference" - }, - { - "name": "specimen", - "type": "reference" - }, - { - "name": "status", - "type": "token" - } - ] - }, - { - "type": "FamilyMemberHistory", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-FamilyMemberHistory", - "documentation": "Endpoints for interacting with FamilyMemberHistory resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "code", - "type": "token" - }, - { - "name": "date", - "type": "date" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "patient", - "type": "reference" - }, - { - "name": "relationship", - "type": "token" - }, - { - "name": "sex", - "type": "token" - }, - { - "name": "status", - "type": "token" - } - ] - }, - { - "type": "Observation", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation", - "documentation": "Endpoints for interacting with Observation resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "based-on", - "type": "reference" - }, - { - "name": "category", - "type": "token" - }, - { - "name": "code", - "type": "token" - }, - { - "name": "component-code", - "type": "token" - }, - { - "name": "data-absent-reason", - "type": "token" - }, - { - "name": "date", - "type": "date" - }, - { - "name": "focus", - "type": "reference" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "subject", - "type": "reference" - }, - { - "name": "performer", - "type": "reference" - }, - { - "name": "specimen", - "type": "reference" - }, - { - "name": "value-string", - "type": "string" - }, - { - "name": "status", - "type": "token" - } - ] - }, - { - "type": "Patient", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient", - "documentation": "Endpoints for interacting with Patient resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "address", - "type": "string" - }, - { - "name": "birthdate", - "type": "date" - }, - { - "name": "death-date", - "type": "token" - }, - { - "name": "gender", - "type": "token" - }, - { - "name": "general-practitioner", - "type": "reference" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "link", - "type": "reference" - }, - { - "name": "name", - "type": "string" - }, - { - "name": "organization", - "type": "reference" - }, - { - "name": "telecom", - "type": "token" - } - ] - }, - { - "type": "Consent", - "profile": "http://hl7.org/fhir/StructureDefinition/Consent", - "documentation": "Endpoints for interacting with Consent resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "action", - "type": "token" - }, - { - "name": "actor", - "type": "reference" - }, - { - "name": "category", - "type": "token" - }, - { - "name": "consentor", - "type": "reference" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "organization", - "type": "reference" - }, - { - "name": "patient", - "type": "reference" - }, - { - "name": "period", - "type": "date" - } - ] - }, - { - "type": "Condition", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Condition", - "documentation": "Endpoints for interacting with Condition resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "asserter", - "type": "reference" - }, - { - "name": "category", - "type": "token" - }, - { - "name": "clinical-status", - "type": "token" - }, - { - "name": "code", - "type": "token" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "onset-info", - "type": "string" - }, - { - "name": "subject", - "type": "reference" - }, - { - "name": "recorded-date", - "type": "date" - }, - { - "name": "severity", - "type": "token" - }, - { - "name": "stage", - "type": "token" - }, - { - "name": "verification-status", - "type": "token" - } - ] - }, - { - "type": "ResearchSubject", - "profile": "http://hl7.org/fhir/StructureDefinition/ResearchSubject" - }, - { - "type": "RelatedPerson", - "profile": "https://fhir.nhs.uk/StructureDefinition/NHSDigital-RelatedPerson-Genomics", - "documentation": "Endpoints for interacting with RelatedPerson resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "patient", - "type": "reference" - }, - { - "name": "relationship", - "type": "token" - } - ] - }, - { - "type": "Specimen", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Specimen", - "documentation": "Endpoints for interacting with Specimen resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update", - "documentation": "To enable updates to specimens" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create", - "documentation": "To allow a user to add a Specimen, which should also be added to the relevant ServiceRequest/Task through a PUT" - }, - { - "code": "search-type", - "documentation": "To enable a user to retrieve specimens, enables specimen tracking" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "accession", - "type": "token" - }, - { - "name": "bodysite", - "type": "token" - }, - { - "name": "collected", - "type": "date" - }, - { - "name": "collector", - "type": "reference" - }, - { - "name": "container-id", - "type": "token" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "parent", - "type": "reference" - }, - { - "name": "subject", - "type": "reference" - }, - { - "name": "status", - "type": "token" - }, - { - "name": "type", - "type": "token" - } - ] - }, - { - "type": "Questionnaire", - "profile": "http://hl7.org/fhir/StructureDefinition/Questionnaire", - "documentation": "For searching supported Questionnaires", - "interaction": [ - { - "code": "read" - }, - { - "code": "search-type" - } - ], - "searchParam": [ - { - "name": "date", - "type": "date" - }, - { - "name": "description", - "type": "string" - }, - { - "name": "effective", - "type": "date" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "name", - "type": "string" - }, - { - "name": "status", - "type": "token" - }, - { - "name": "title", - "type": "string" - }, - { - "name": "version", - "type": "token" - } - ] - }, - { - "type": "QuestionnaireResponse", - "profile": "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse", - "documentation": "Endpoints for interacting with QuestionnaireResponse resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "author", - "type": "reference" - }, - { - "name": "authored", - "type": "date" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "subject", - "type": "reference" - }, - { - "name": "questionnaire", - "type": "reference" - }, - { - "name": "source", - "type": "reference" - }, - { - "name": "status", - "type": "token" - } - ] - }, - { - "type": "OperationDefinition", - "profile": "https://hl7.org/fhir/StructureDefinition/OperationDefinition" - }, - { - "type": "OperationOutcome", - "profile": "http://hl7.org/fhir/StructureDefinition/OperationOutcome", - "documentation": "For searching historical OperationOutcomes", - "interaction": [ - { - "code": "read" - }, - { - "code": "search-type" - } - ] - }, - { - "type": "BodyStructure", - "profile": "http://hl7.org/fhir/StructureDefinition/BodyStructure", - "documentation": "Endpoints for interacting with BodyStructure resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "identifier", - "type": "token" - }, - { - "name": "location", - "type": "token" - }, - { - "name": "morphology", - "type": "token" - }, - { - "name": "patient", - "type": "reference" - } - ] - }, - { - "type": "Provenance", - "profile": "http://hl7.org/fhir/StructureDefinition/Provenance", - "documentation": "For searching stored Provenance resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "search-type" - } - ], - "searchParam": [ - { - "name": "agent", - "type": "reference" - }, - { - "name": "entity", - "type": "reference" - }, - { - "name": "target", - "type": "reference" - }, - { - "name": "recorded", - "type": "date" - } - ] - } - ] - } - ] + "resourceType": "CapabilityStatement", + "id": "CapabilityStatement-genomics-application", + "url": "https://fhir.nhs.uk/CapabilityStatement/CapabilityStatement-genomics-application", + "version": "0.1.0", + "name": "CapabilityStatementGenomicsApplication", + "status": "draft", + "date": "2023-02-27T00:00:00+00:00", + "publisher": "NHS England", + "description": "Sample server capability for the Genomic Medicine Service", + "kind": "instance", + "implementationGuide": [ + "https://simplifier.net/guide/fhir-genomics-implementation-guide", + "https://simplifier.net/guide/nhsdigital" + ], + "fhirVersion": "4.0.1", + "format": [ + "application/fhir+json" + ], + "implementation": { + "description": "Exemplar CapabilityStatement for the GMS central broker implementation" + }, + "messaging": [ + { + "endpoint": [ + { + "protocol": { + "system": "http://terminology.hl7.org/CodeSystem/message-transport", + "code": "http", + "display": "HTTP" + }, + "address": "https://[baseUrl]/$process-message" + } + ], + "documentation": "Endpoint which accepts test order and result message bundles. The server saves the whole message as well as splitting the message into its individual resources for ease of updating through RESTful interactions", + "supportedMessage": [ + { + "mode": "receiver", + "definition": "https://fhir.nhs.uk/MessageDefinition/genomic-test-request" + }, + { + "mode": "receiver", + "definition": "https://fhir.nhs.uk/MessageDefinition/genomic-test-response" + } + ] + } + ], + "rest": [ + { + "mode": "server", + "documentation": "RESTful endpoints supported by the Genomic Medicine Service", + "security": { + "service": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/restful-security-service", + "code": "OAuth", + "display": "OAuth2 Token" + } + ] + } + ] + }, + "resource": [ + { + "type": "AuditEvent", + "profile": "http://hl7.org/fhir/StructureDefinition/AuditEvent", + "documentation": "For searching recorded AuditEvents", + "interaction": [ + { + "code": "read" + }, + { + "code": "search-type" + } + ], + "searchParam": [ + { + "name": "action", + "type": "token" + }, + { + "name": "agent", + "type": "reference" + }, + { + "name": "date", + "type": "date" + }, + { + "name": "entity", + "type": "reference" + }, + { + "name": "outcome", + "type": "token" + }, + { + "name": "patient", + "type": "reference" + } + ] + }, + { + "type": "Bundle", + "profile": "http://hl7.org/fhir/StructureDefinition/Bundle", + "documentation": "For posting FHIR transaction bundles (http://hl7.org/fhir/R4B/http.html#transaction) to the server.", + "interaction": [ + { + "code": "create", + "documentation": "Bundle containing ServiceRequest and all supporting resources (Patient, PractitionerRole, Specimen, etc.)" + } + ], + "conditionalCreate": true, + "referencePolicy": [ + "resolves" + ] + }, + { + "type": "CodeSystem", + "profile": "http://hl7.org/fhir/StructureDefinition/CodeSystem", + "documentation": "For searching supported CodeSystems", + "interaction": [ + { + "code": "read" + }, + { + "code": "search-type" + } + ], + "searchParam": [ + { + "name": "code", + "type": "token" + }, + { + "name": "context", + "type": "token" + }, + { + "name": "description", + "type": "string" + }, + { + "name": "identifier", + "type": "token" + }, + { + "name": "name", + "type": "string" + }, + { + "name": "system", + "type": "uri" + }, + { + "name": "title", + "type": "string" + } + ] + }, + { + "type": "ConceptMap", + "profile": "http://hl7.org/fhir/StructureDefinition/ConceptMap", + "documentation": "For searching provided ConceptMaps", + "interaction": [ + { + "code": "read" + }, + { + "code": "search-type" + } + ], + "searchParam": [ + { + "name": "context", + "type": "token" + }, + { + "name": "description", + "type": "string" + }, + { + "name": "identifier", + "type": "token" + }, + { + "name": "name", + "type": "string" + }, + { + "name": "source-system", + "type": "uri" + }, + { + "name": "target-system", + "type": "uri" + }, + { + "name": "title", + "type": "string" + } + ] + }, + { + "type": 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"versioned", + "readHistory": true, + "conditionalCreate": true, + "referencePolicy": [ + "resolves" + ], + "searchParam": [ + { + "name": "patient", + "type": "reference" + }, + { + "name": "relationship", + "type": "token" + } + ] + }, + { + "type": "Specimen", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Specimen", + "documentation": "Endpoints for interacting with Specimen resources", + "interaction": [ + { + "code": "read" + }, + { + "code": "vread" + }, + { + "code": "update", + "documentation": "To enable updates to specimens" + }, + { + "code": "patch" + }, + { + "code": "delete" + }, + { + "code": "history-instance" + }, + { + "code": "create", + "documentation": "To allow a user to add a Specimen, which should also be added to the relevant ServiceRequest/Task through a PUT" + }, + { + "code": "search-type", + "documentation": "To enable a user to retrieve specimens, enables specimen tracking" + } + ], + "versioning": "versioned", + "readHistory": true, + "conditionalCreate": true, + "referencePolicy": [ + "resolves" + ], + "searchParam": [ + { + "name": "accession", + "type": "token" + }, + { + "name": "bodysite", + "type": "token" + }, + { + "name": "collected", + "type": "date" + }, + { + "name": "collector", + "type": "reference" + }, + { + "name": "container-id", + "type": "token" + }, + { + "name": "identifier", + "type": "token" + }, + { + "name": "parent", + "type": "reference" + }, + { + "name": "subject", + "type": "reference" + }, + { + "name": "status", + "type": "token" + }, + { + "name": "type", + "type": "token" + } + ] + }, + { + "type": "Questionnaire", + "profile": "http://hl7.org/fhir/StructureDefinition/Questionnaire", + "documentation": "For searching supported Questionnaires", + "interaction": [ + { + "code": "read" + }, + { + "code": "search-type" + } + ], + "searchParam": [ + { + "name": "date", + "type": "date" + }, + { + "name": "description", + "type": "string" + }, + { + "name": "effective", + "type": "date" + }, + { + "name": "identifier", + "type": "token" + }, + { + "name": "name", + "type": "string" + }, + { + "name": "status", + "type": "token" + }, + { + "name": "title", + "type": "string" + }, + { + "name": "version", + "type": "token" + } + ] + }, + { + "type": "QuestionnaireResponse", + "profile": "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse", + "documentation": "Endpoints for interacting with QuestionnaireResponse resources", + "interaction": [ + { + "code": "read" + }, + { + "code": "vread" + }, + { + "code": "update" + }, + { + "code": "patch" + }, + { + "code": "delete" + }, + { + "code": "history-instance" + }, + { + "code": "create" + }, + { + "code": "search-type" + } + ], + "versioning": "versioned", + "readHistory": true, + "conditionalCreate": true, + "referencePolicy": [ + "resolves" + ], + "searchParam": [ + { + "name": "author", + "type": "reference" + }, + { + "name": "authored", + "type": "date" + }, + { + "name": "identifier", + "type": "token" + }, + { + "name": "subject", + "type": "reference" + }, + { + "name": "questionnaire", + "type": "reference" + }, + { + "name": "source", + "type": "reference" + }, + { + "name": "status", + "type": "token" + } + ] + }, + { + "type": "OperationDefinition", + "profile": "https://hl7.org/fhir/StructureDefinition/OperationDefinition" + }, + { + "type": "OperationOutcome", + "profile": "http://hl7.org/fhir/StructureDefinition/OperationOutcome", + "documentation": "For searching historical OperationOutcomes", + "interaction": [ + { + "code": "read" + }, + { + "code": "search-type" + } + ] + }, + { + "type": "DocumentReference", + "profile": "https://hl7.org/fhir/StructureDefinition/DocumentReference", + "supportedProfile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-data-file" + ], + "documentation": "Endpoints for interacting with DocumentReference resources", + "interaction": [ + { + "code": "read" + }, + { + "code": "vread" + }, + { + "code": "update" + }, + { + "code": "patch" + }, + { + "code": "delete" + }, + { + "code": "history-instance" + }, + { + "code": "create" + }, + { + "code": "search-type" + } + ], + "versioning": "versioned", + "readHistory": true, + "conditionalCreate": true, + "referencePolicy": [ + "resolves" + ], + "searchParam": [ + { + "name": "authenticator", + "type": "reference" + }, + { + "name": "author", + "type": "reference" + }, + { + "name": "category", + "type": "token" + }, + { + "name": "contenttype", + "type": "token" + }, + { + "name": "custodian", + "type": "reference" + }, + { + "name": "date", + "type": "date" + }, + { + "name": "identifier", + "type": "token" + }, + { + "name": "location", + "type": "uri" + }, + { + "name": "related", + "type": "reference" + }, + { + "name": "relatesto", + "type": "reference" + }, + { + "name": "status", + "type": "token" + }, + { + "name": "subject", + "type": "reference" + }, + { + "name": "type", + "type": "token" + } + ] + }, + { + "type": "BodyStructure", + "profile": "http://hl7.org/fhir/StructureDefinition/BodyStructure", + "documentation": "Endpoints for interacting with BodyStructure resources", + "interaction": [ + { + "code": "read" + }, + { + "code": "vread" + }, + { + "code": "update" + }, + { + "code": "patch" + }, + { + "code": "delete" + }, + { + "code": "history-instance" + }, + { + "code": "create" + }, + { + "code": "search-type" + } + ], + "versioning": "versioned", + "readHistory": true, + "conditionalCreate": true, + "referencePolicy": [ + "resolves" + ], + "searchParam": [ + { + "name": "identifier", + "type": "token" + }, + { + "name": "location", + "type": "token" + }, + { + "name": "morphology", + "type": "token" + }, + { + "name": "patient", + "type": "reference" + } + ] + }, + { + "type": "Provenance", + "profile": "http://hl7.org/fhir/StructureDefinition/Provenance", + "documentation": "For searching stored Provenance resources", + "interaction": [ + { + "code": "read" + }, + { + "code": "search-type" + } + ], + "searchParam": [ + { + "name": "agent", + "type": "reference" + }, + { + "name": "entity", + "type": "reference" + }, + { + "name": "target", + "type": "reference" + }, + { + "name": "recorded", + "type": "date" + } + ] + } + ] + } + ] } \ No newline at end of file diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 2b8ad7b1..ba00cb90 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -2,9 +2,9 @@ "updated": "2024-05-16T09:14:29.5276199+01:00", "dependencies": { "fhir.r4.ukcore.stu2": "2.0.0", - "hl7.fhir.r4.core": "4.0.1" + "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.uv.genomics-reporting": "3.0.1-SNAPSHOT" }, "missing": { - "hl7.fhir.uv.genomics-reporting": "3.0.1-SNAPSHOT" } } From 3ae552132a47ab3d6e28fd0093bfeb16c3e0de23 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Thu, 16 May 2024 10:10:09 +0100 Subject: [PATCH 05/21] Addition of supportedProfiles to requirements CS --- ...bilityStatement-genomics-requirements.json | 366 ++++++++++-------- 1 file changed, 199 insertions(+), 167 deletions(-) diff --git a/CapabilityStatement/CapabilityStatement-genomics-requirements.json b/CapabilityStatement/CapabilityStatement-genomics-requirements.json index 917c142c..7f889e5c 100644 --- a/CapabilityStatement/CapabilityStatement-genomics-requirements.json +++ b/CapabilityStatement/CapabilityStatement-genomics-requirements.json @@ -1,169 +1,201 @@ { - "resourceType": "CapabilityStatement", - "id": "genomics-requirements", - "url": "https://fhir.nhs.uk/CapabilityStatement/genomics-requirements", - "version": "0.1.0", - "name": "GenomicsRequirements", - "status": "draft", - "date": "2022-11-25T00:00:00+00:00", - "publisher": "digital.nhs.uk", - "description": "Conformance requirements for NHS Digital Genomics Implementation Guide", - "kind": "requirements", - "fhirVersion": "4.0.1", - "format": [ - "application/fhir+json", - "application/fhir+xml" - ], - "rest": [ - { - "mode": "server", - "security": { - "service": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/restful-security-service", - "code": "OAuth", - "display": "OAuth2 Token" - } - ] - } - ] - }, - "resource": [ - { - "type": "AuditEvent", - "profile": "http://hl7.org/fhir/StructureDefinition/AuditEvent" - }, - { - "type": "Bundle", - "profile": "http://hl7.org/fhir/StructureDefinition/Bundle" - }, - { - "type": "CodeSystem", - "profile": "http://hl7.org/fhir/StructureDefinition/CodeSystem" - }, - { - "type": "ConceptMap", - "profile": "http://hl7.org/fhir/StructureDefinition/ConceptMap" - }, - { - "type": "HealthcareService", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-HealthcareService" - }, - { - "type": "MessageDefinition", - "profile": "http://hl7.org/fhir/StructureDefinition/MessageDefinition" - }, - { - "type": "NamingSystem", - "profile": "http://hl7.org/fhir/StructureDefinition/NamingSystem" - }, - { - "type": "Parameters", - "profile": "http://hl7.org/fhir/StructureDefinition/Parameters" - }, - { - "type": "StructureMap", - "profile": "http://hl7.org/fhir/StructureDefinition/StructureMap" - }, - { - "type": "ValueSet", - "profile": "http://hl7.org/fhir/StructureDefinition/ValueSet" - }, - { - "type": "MessageHeader", - "profile": "http://hl7.org/fhir/StructureDefinition/MessageHeader" - }, - { - "type": "Subscription", - "profile": "http://hl7.org/fhir/StructureDefinition/Subscription" - }, - { - "type": "CapabilityStatement", - "profile": "http://hl7.org/fhir/StructureDefinition/CapabilityStatement" - }, - { - "type": "Task", - "profile": "http://hl7.org/fhir/StructureDefinition/Task" - }, - { - "type": "ServiceRequest", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-ServiceRequest" - }, - { - "type": "PractitionerRole", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-PractitionerRole" - }, - { - "type": "Practitioner", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Practitioner" - }, - { - "type": "Organization", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization" - }, - { - "type": "DiagnosticReport", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport" - }, - { - "type": "FamilyMemberHistory", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-FamilyMemberHistory" - }, - { - "type": "Observation", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation" - }, - { - "type": "Patient", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient" - }, - { - "type": "Consent", - "profile": "http://hl7.org/fhir/StructureDefinition/Consent" - }, - { - "type": "Condition", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Condition" - }, - { - "type": "ResearchSubject", - "profile": "http://hl7.org/fhir/StructureDefinition/ResearchSubject" - }, - { - "type": "RelatedPerson", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-RelatedPerson" - }, - { - "type": "Specimen", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Specimen" - }, - { - "type": "Questionnaire", - "profile": "http://hl7.org/fhir/StructureDefinition/Questionnaire" - }, - { - "type": "QuestionnaireResponse", - "profile": "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" - }, - { - "type": "OperationDefinition", - "profile": "http://hl7.org/fhir/StructureDefinition/OperationDefinition" - }, - { - "type": "OperationOutcome", - "profile": "http://hl7.org/fhir/StructureDefinition/OperationOutcome" - }, - { - "type": "BodyStructure", - "profile": "http://hl7.org/fhir/StructureDefinition/BodyStructure" - }, - { - "type": "Provenance", - "profile": "http://hl7.org/fhir/StructureDefinition/Provenance" - } - ] - } - ] + "resourceType": "CapabilityStatement", + "id": "genomics-requirements", + "url": "https://fhir.nhs.uk/CapabilityStatement/genomics-requirements", + "version": "0.1.0", + "name": "GenomicsRequirements", + "status": "draft", + "date": "2022-11-25T00:00:00+00:00", + "publisher": "digital.nhs.uk", + "description": "Conformance requirements for NHS Digital Genomics Implementation Guide", + "kind": "requirements", + "fhirVersion": "4.0.1", + "format": [ + "application/fhir+json", + "application/fhir+xml" + ], + "rest": [ + { + "mode": "server", + "security": { + "service": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/restful-security-service", + "code": "OAuth", + "display": "OAuth2 Token" + } + ] + } + ] + }, + "resource": [ + { + "type": "AuditEvent", + "profile": "http://hl7.org/fhir/StructureDefinition/AuditEvent" + }, + { + "type": "Bundle", + "profile": "http://hl7.org/fhir/StructureDefinition/Bundle" + }, + { + "type": "CodeSystem", + "profile": "http://hl7.org/fhir/StructureDefinition/CodeSystem" + }, + { + "type": "ConceptMap", + "profile": "http://hl7.org/fhir/StructureDefinition/ConceptMap" + }, + { + "type": "HealthcareService", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-HealthcareService" + }, + { + "type": "MessageDefinition", + "profile": "http://hl7.org/fhir/StructureDefinition/MessageDefinition" + }, + { + "type": "NamingSystem", + "profile": "http://hl7.org/fhir/StructureDefinition/NamingSystem" + }, + { + "type": "Parameters", + "profile": "http://hl7.org/fhir/StructureDefinition/Parameters" + }, + { + "type": "StructureMap", + "profile": "http://hl7.org/fhir/StructureDefinition/StructureMap" + }, + { + "type": "ValueSet", + "profile": "http://hl7.org/fhir/StructureDefinition/ValueSet" + }, + { + "type": "MessageHeader", + "profile": "http://hl7.org/fhir/StructureDefinition/MessageHeader" + }, + { + "type": "Subscription", + "profile": "http://hl7.org/fhir/StructureDefinition/Subscription" + }, + { + "type": "CapabilityStatement", + "profile": "http://hl7.org/fhir/StructureDefinition/CapabilityStatement" + }, + { + "type": "Task", + "profile": "http://hl7.org/fhir/StructureDefinition/Task", + "supportedProfile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation", + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation" + ] + }, + { + "type": "ServiceRequest", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-ServiceRequest" + }, + { + "type": "PractitionerRole", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-PractitionerRole" + }, + { + "type": "Practitioner", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Practitioner" + }, + { + "type": "Organization", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization" + }, + { + "type": "DiagnosticReport", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport", + "supportedProfile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report" + ] + }, + { + "type": "FamilyMemberHistory", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-FamilyMemberHistory" + }, + { + "type": "Observation", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation", + "supportedProfile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication", + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype", + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype", + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker", + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence", + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship", + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication", + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + { + "type": "Procedure", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Procedure", + "supportedProfile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study", + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis" + ] + } + { + "type": "Patient", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient" + }, + { + "type": "Consent", + "profile": "http://hl7.org/fhir/StructureDefinition/Consent" + }, + { + "type": "Condition", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Condition" + }, + { + "type": "ResearchSubject", + "profile": "http://hl7.org/fhir/StructureDefinition/ResearchSubject" + }, + { + "type": "RelatedPerson", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-RelatedPerson" + }, + { + "type": "Specimen", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Specimen" + }, + { + "type": "Questionnaire", + "profile": "http://hl7.org/fhir/StructureDefinition/Questionnaire" + }, + { + "type": "QuestionnaireResponse", + "profile": "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" + }, + { + "type": "OperationDefinition", + "profile": "http://hl7.org/fhir/StructureDefinition/OperationDefinition" + }, + { + "type": "OperationOutcome", + "profile": "http://hl7.org/fhir/StructureDefinition/OperationOutcome" + }, + { + "type": "BodyStructure", + "profile": "http://hl7.org/fhir/StructureDefinition/BodyStructure" + }, + { + "type": "DocumentReference", + "profile": "https://hl7.org/fhir/StructureDefinition/DocumentReference", + "supportedProfile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-data-file" + ] + } + { + "type": "Provenance", + "profile": "http://hl7.org/fhir/StructureDefinition/Provenance" + } + ] + } + ] } \ No newline at end of file From 0789e08728cbe4253f4e2e9058e436a223076079 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Thu, 16 May 2024 10:26:59 +0100 Subject: [PATCH 06/21] Update UK Genomic Reporting dependency downgrade to 3.0.0-ballot version available on Simplifier --- fhirpkg.lock.json | 9 +++++---- package.json | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index ba00cb90..5cdf25ac 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,10 +1,11 @@ { - "updated": "2024-05-16T09:14:29.5276199+01:00", + "updated": "2024-05-16T10:18:19.8963748+01:00", "dependencies": { "fhir.r4.ukcore.stu2": "2.0.0", "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.genomics-reporting": "3.0.1-SNAPSHOT" + "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", + "hl7.terminology.r4": "5.3.0", + "hl7.fhir.uv.extensions.r4": "1.0.0" }, - "missing": { - } + "missing": {} } diff --git a/package.json b/package.json index 475d5531..dccadfa2 100644 --- a/package.json +++ b/package.json @@ -9,6 +9,6 @@ "dependencies": { "fhir.r4.ukcore.stu2": "2.0.0", "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.genomics-reporting": "3.0.1-SNAPSHOT" + "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot" } } From 24268a167e0dea083849a63b88003a2b17ce9de8 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 16 May 2024 15:02:16 +0100 Subject: [PATCH 07/21] Add DR Resource DiagnosticReport --- ...eport-GenomicReport-VariantAssessment.json | 117 ++++++++++++++++++ .../Observation-GenomicsVariant-SLC52A2.json | 2 +- 2 files changed, 118 insertions(+), 1 deletion(-) create mode 100644 DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json diff --git a/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json new file mode 100644 index 00000000..2871bf76 --- /dev/null +++ b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json @@ -0,0 +1,117 @@ +{ + "resourceType": "DiagnosticReport", + "id": "DiagnosticReport-GenomicReport-VariantAssessment", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report" + ] + }, + "extension": [ + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-reference", + "valueReference": { + "reference": "Procedure/Procedure-GenomicsReport-GenomicStudy" + } + }, + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action", + "valueReference": { + "reference": "Task/Task-GenomicReport-MedicationRecommendation", + "display": "Confirmatory testing recommended" + } + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact", + "valueRelatedArtifact": { + "type": "citation", + "display": "Johnson et al 2012 (PMID22740598)" + } + + }, + { + "url": "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact", + "valueRelatedArtifact": { + "type": "citation", + "display": "Foley et al 2014 (PMID22740598)" + } + + }, + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note", + "valueAnnotation": { + "extension": [ + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/coded-annotation-types-cs", + "code": "test-disclaimer" + } + ] + } + } + ], + "text": "This test was developed and its performance determined by this laboratory. It has not been cleared or approved by UK Food and Drug Administration.\nSince FDA Approval is not required for clinical use of this test, this laboratory has established and validated the test's accuracy and precision,\npursuant to the requirement of CLIA '88. This laboratory is licensed and/or accredited under CLIA and CAP (CAP# xxxxxxx / CLIA# xxxxxxxxxx)." + } + } + ], + "basedOn": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0074", + "code": "GE" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51969-4" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example" + }, + "effectiveDateTime": "2023-09-16T00:00:00-05:00", + "issued": "2023-10-16T00:00:00-05:00", + "performer": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "R0A" + } + } + ], + "result": [ + { + "reference": "Observation/Observation-GenomicsVariant-SLC52A2", + "display": "Brown-Vialetto-Van Laere syndrome type 2" + }, + { + "reference": "Observation/Observation-GenomicImplication-Therapeutic" + } + ], + "conclusion": "Pheobe is homozygous for a pathogenic SLC52A2 missense variant (details below) previously reported by Johnson et al 2012 (PMID22740598). Biallelic pathogenic SLC52A2 variants cause autosomal recessive Brown-Vialetto-Van Laere syndrome type 2 (MIM614707).", + "conclusionCode": [ + { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6576-8", + "display": "Positive" + } + ] + } + ] +} \ No newline at end of file diff --git a/Observation/Observation-GenomicsVariant-SLC52A2.json b/Observation/Observation-GenomicsVariant-SLC52A2.json index 4a97895f..23f80ed6 100644 --- a/Observation/Observation-GenomicsVariant-SLC52A2.json +++ b/Observation/Observation-GenomicsVariant-SLC52A2.json @@ -90,7 +90,7 @@ "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org", + "system": "http://www.genenames.org/", "code": "HGNC:30224", "display": "SLC52A2" } From 0cdb15b6fdd184c459db5485c92695cd044657ec Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 16 May 2024 16:58:05 +0100 Subject: [PATCH 08/21] Less Strict Validation Less Strict Validation --- Observation/Observation-GenomicImplication-Therapeutic.json | 6 +++--- options.json | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Observation/Observation-GenomicImplication-Therapeutic.json b/Observation/Observation-GenomicImplication-Therapeutic.json index 57fbd04d..14be8f5e 100644 --- a/Observation/Observation-GenomicImplication-Therapeutic.json +++ b/Observation/Observation-GenomicImplication-Therapeutic.json @@ -84,9 +84,9 @@ "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "9346", - "display": "riboflavin" + "system": "http://snomed.info/sct", + "code": "777436008", + "display": "Riboflavin" } ] } diff --git a/options.json b/options.json index ac6548a1..74e57a59 100644 --- a/options.json +++ b/options.json @@ -1,5 +1,5 @@ { - "strict-validation": true, + "strict-validation": false, "ignore-folders": [], "ignore-files": [], "error-if-metaProfile-present": false From fd8025405e48603334384a7b1396d4d8b5f8fc92 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Fri, 17 May 2024 13:56:32 +0100 Subject: [PATCH 09/21] Remove Reference to HGVS ValueSet Remove Reference to HGVS ValueSet --- .../Observation-GenomicsVariant-SLC52A2.json | 18 ------------------ options.json | 2 +- 2 files changed, 1 insertion(+), 19 deletions(-) diff --git a/Observation/Observation-GenomicsVariant-SLC52A2.json b/Observation/Observation-GenomicsVariant-SLC52A2.json index 23f80ed6..9a3a3510 100644 --- a/Observation/Observation-GenomicsVariant-SLC52A2.json +++ b/Observation/Observation-GenomicsVariant-SLC52A2.json @@ -135,24 +135,6 @@ ] } }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81290-9" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://varnomen.hgvs.org", - "code": "NM_001363118.2:c.916G>A" - } - ] - } - }, { "code": { "coding": [ diff --git a/options.json b/options.json index 74e57a59..ac6548a1 100644 --- a/options.json +++ b/options.json @@ -1,5 +1,5 @@ { - "strict-validation": false, + "strict-validation": true, "ignore-folders": [], "ignore-files": [], "error-if-metaProfile-present": false From e1b86b30badae6144784f40fd5d73569bee52547 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Wed, 22 May 2024 09:30:59 +0100 Subject: [PATCH 10/21] Add Reference to HGVS ValueSet http://varnomen.hgvs.org --- ...Report-GenomicReport-VariantAssessment.json | 6 ------ .../Observation-GenomicsVariant-SLC52A2.json | 18 ++++++++++++++++++ 2 files changed, 18 insertions(+), 6 deletions(-) diff --git a/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json index 2871bf76..e42424a7 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json +++ b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json @@ -7,12 +7,6 @@ ] }, "extension": [ - { - "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-reference", - "valueReference": { - "reference": "Procedure/Procedure-GenomicsReport-GenomicStudy" - } - }, { "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action", "valueReference": { diff --git a/Observation/Observation-GenomicsVariant-SLC52A2.json b/Observation/Observation-GenomicsVariant-SLC52A2.json index 9a3a3510..23f80ed6 100644 --- a/Observation/Observation-GenomicsVariant-SLC52A2.json +++ b/Observation/Observation-GenomicsVariant-SLC52A2.json @@ -135,6 +135,24 @@ ] } }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81290-9" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://varnomen.hgvs.org", + "code": "NM_001363118.2:c.916G>A" + } + ] + } + }, { "code": { "coding": [ From de518d8e8713f4c7dfa8f6f9c963d32be14a8823 Mon Sep 17 00:00:00 2001 From: Ryan May <112563297+ryma2fhir@users.noreply.github.com> Date: Wed, 22 May 2024 12:05:42 +0100 Subject: [PATCH 11/21] Update options.json --- options.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/options.json b/options.json index ac6548a1..15f98d2b 100644 --- a/options.json +++ b/options.json @@ -1,6 +1,6 @@ { - "strict-validation": true, + "strict-validation": false, "ignore-folders": [], "ignore-files": [], "error-if-metaProfile-present": false -} \ No newline at end of file +} From 1fe87d539c3a4f0362dc4499b1ac0be65d9e8a22 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Wed, 22 May 2024 13:13:00 +0100 Subject: [PATCH 12/21] Remove Procedure-GenomicsReport-GenomicStudy --- ...Procedure-GenomicsReport-GenomicStudy.json | 33 ------------------- ...GenomicReport-FollowupRecommendation.json} | 0 2 files changed, 33 deletions(-) delete mode 100644 Procedure/Procedure-GenomicsReport-GenomicStudy.json rename Task/{Task-GenomicReport-MedicationRecommendation.json => Task-GenomicReport-FollowupRecommendation.json} (100%) diff --git a/Procedure/Procedure-GenomicsReport-GenomicStudy.json b/Procedure/Procedure-GenomicsReport-GenomicStudy.json deleted file mode 100644 index 11586e65..00000000 --- a/Procedure/Procedure-GenomicsReport-GenomicStudy.json +++ /dev/null @@ -1,33 +0,0 @@ -{ - "resourceType" : "Procedure", - "id" : "Procedure-GenomicsReport-GenomicStudy", - "meta" : { - "profile" : ["http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study"] - }, - "basedOn" : [{ - "reference" : "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" - }], - "status" : "completed", - "category" : { - "coding" : [{ - "system" : "http://terminology.hl7.org/CodeSystem/observation-category", - "code" : "laboratory" - }] - }, - "code" : { - "coding" : [ - { - "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs", - "code" : "struc-var", - "display" : "Structural variation detection" - } - ] - }, - "subject" : { - "reference" : "Patient/Patient-PheobeSmitham-Example" - }, - "performedDateTime" : "2023-09-16", - "note" : [{ - "text" : "Proband whole genome sequencing by the 100,000 Genomics Project with analysis of the PanelApp Paediatric motor neuronopathies (version 1.6) gene panel followed by in-house Sanger sequencing confirmation. Please note that the sensitivity of this test is limited by the types of detectable pathogenic variants, regions of low read depth coverage and incomplete ascertainment of disease-gene associations. Further information including read depth coverage is available on request. *Variants are classified using the ACMG/AMP guidelines (Richards et al 2015 PMID25741868)." - }] -} \ No newline at end of file diff --git a/Task/Task-GenomicReport-MedicationRecommendation.json b/Task/Task-GenomicReport-FollowupRecommendation.json similarity index 100% rename from Task/Task-GenomicReport-MedicationRecommendation.json rename to Task/Task-GenomicReport-FollowupRecommendation.json From 41f4d5a066e0b5c5317f23fd719d709247ba675b Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Wed, 22 May 2024 13:22:27 +0100 Subject: [PATCH 13/21] Remove Procedure-GenomicsReport-GenomicStudy --- .../DiagnosticReport-GenomicReport-VariantAssessment.json | 2 +- Task/Task-GenomicReport-FollowupRecommendation.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json index e42424a7..734f1937 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json +++ b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json @@ -10,7 +10,7 @@ { "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action", "valueReference": { - "reference": "Task/Task-GenomicReport-MedicationRecommendation", + "reference": "Task/Task-GenomicReport-FollowupRecommendation", "display": "Confirmatory testing recommended" } }, diff --git a/Task/Task-GenomicReport-FollowupRecommendation.json b/Task/Task-GenomicReport-FollowupRecommendation.json index 9531418e..d25b1390 100644 --- a/Task/Task-GenomicReport-FollowupRecommendation.json +++ b/Task/Task-GenomicReport-FollowupRecommendation.json @@ -1,6 +1,6 @@ { "resourceType" : "Task", - "id" : "Task-GenomicReport-MedicationRecommendation", + "id" : "Task-GenomicReport-FollowupRecommendation", "meta" : { "profile" : [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation" From fa4a214389c052fc290eb6f7bb80bffc2cc553fb Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 23 May 2024 18:06:31 +0100 Subject: [PATCH 14/21] Add Genomic Test Panel Codes Add Genomic Test Panel Codes --- .../England-GenomicTestPanelCodes.json | 43 +++++++++++++++++++ .../Observation-GenomicsVariant-SLC52A2.json | 18 -------- 2 files changed, 43 insertions(+), 18 deletions(-) create mode 100644 NamingSystem/England-GenomicTestPanelCodes.json diff --git a/NamingSystem/England-GenomicTestPanelCodes.json b/NamingSystem/England-GenomicTestPanelCodes.json new file mode 100644 index 00000000..a7cfb037 --- /dev/null +++ b/NamingSystem/England-GenomicTestPanelCodes.json @@ -0,0 +1,43 @@ +{ + "resourceType": "NamingSystem", + "id": "England-GenomicTestPanelCodes", + "name": "EnglandGenomicTestPanelCodes", + "status": "draft", + "kind": "codesystem", + "date": "2023-05-23", + "publisher": "NHS England", + "contact": [ + { + "name": "NHS England", + "telecom": [ + { + "system": "email", + "value": "interoperabilityteam@nhs.net", + "use": "work", + "rank": 1 + } + ] + }, + { + "name": "NHS Genomic Medicine Service", + "telecom": [ + { + "system": "email", + "value": "england.genomics@nhs.net", + "use": "work", + "rank": 1 + } + ] + } + ], + "responsible": "NHS Genomic Interop Programme", + "description": "NamingSystem for Genomic Test Panel Codes", + "usage": "Used to define the system for Genomic Test Panel codes within ServiceRequest resources", + "uniqueId": [ + { + "type": "uri", + "value": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestPanelCodes", + "preferred": true + } + ] +} \ No newline at end of file diff --git a/Observation/Observation-GenomicsVariant-SLC52A2.json b/Observation/Observation-GenomicsVariant-SLC52A2.json index 23f80ed6..9a3a3510 100644 --- a/Observation/Observation-GenomicsVariant-SLC52A2.json +++ b/Observation/Observation-GenomicsVariant-SLC52A2.json @@ -135,24 +135,6 @@ ] } }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81290-9" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://varnomen.hgvs.org", - "code": "NM_001363118.2:c.916G>A" - } - ] - } - }, { "code": { "coding": [ From b257c402d22d208894b3e75c3aba636d97c0c5a1 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 9 Jan 2025 17:02:37 +0000 Subject: [PATCH 15/21] Add CapabilityStatement-genomics-application. Add CapabilityStatement-genomics-application. --- ...abilityStatement-genomics-application.json | 2111 +++++++++-------- 1 file changed, 1095 insertions(+), 1016 deletions(-) diff --git a/CapabilityStatement/CapabilityStatement-genomics-application.json b/CapabilityStatement/CapabilityStatement-genomics-application.json index 775b985f..93c5d51f 100644 --- a/CapabilityStatement/CapabilityStatement-genomics-application.json +++ b/CapabilityStatement/CapabilityStatement-genomics-application.json @@ -773,1020 +773,1099 @@ "type": "token" }, { - "name": "supporting-info", - "type": "reference" - } - ] - }, - { - "type": "PractitionerRole", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-PractitionerRole", - "documentation": "Endpoints for interacting with PractitionerRole resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "endpoint", - "type": "reference" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "organization", - "type": "reference" - }, - { - "name": "practitioner", - "type": "reference" - }, - { - "name": "specialty", - "type": "token" - }, - { - "name": "telecom", - "type": "token" - } - ] - }, - { - "type": "Practitioner", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Practitioner", - "documentation": "Endpoints for interacting with Practitioner resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "name", - "type": "string" - }, - { - "name": "identifier", - "type": "token" - } - ] - }, - { - "type": "Organization", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization", - "documentation": "Endpoints for interacting with PractitionerRole resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "address", - "type": "string" - }, - { - "name": "endpoint", - "type": "reference" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "name", - "type": "string" - }, - { - "name": "partof", - "type": "reference" - }, - { - "name": "type", - "type": "token" - } - ] - }, - { - "type": "DiagnosticReport", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport", - "documentation": "Endpoints for interacting with DiagnosticReport resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update", - "documentation": "Allows a DiagnosticReport to be updated. Could also be used to notify requesters that a DiagnosticReport has been updated, if proactive notification is implemented." - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create", - "documentation": "Allows a DiagnosticReport to be created on the service. Triggers notification to the requester that a DiagnosticReport is available." - }, - { - "code": "search-type", - "documentation": "Not required for alpha build, but could be used to retrieve historical diagnostic reports." - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "based-on", - "type": "reference" - }, - { - "name": "category", - "type": "token" - }, - { - "name": "code", - "type": "token" - }, - { - "name": "conclusion", - "type": "token" - }, - { - "name": "date", - "type": "date" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "issued", - "type": "date" - }, - { - "name": "subject", - "type": "reference" - }, - { - "name": "performer", - "type": "reference" - }, - { - "name": "result", - "type": "reference" - }, - { - "name": "results-interpreter", - "type": "reference" - }, - { - "name": "specimen", - "type": "reference" - }, - { - "name": "status", - "type": "token" - } - ] - }, - { - "type": "FamilyMemberHistory", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-FamilyMemberHistory", - "documentation": "Endpoints for interacting with FamilyMemberHistory resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "code", - "type": "token" - }, - { - "name": "date", - "type": "date" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "patient", - "type": "reference" - }, - { - "name": "relationship", - "type": "token" - }, - { - "name": "sex", - "type": "token" - }, - { - "name": "status", - "type": "token" - } - ] - }, - { - "type": "Observation", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation", - "documentation": "Endpoints for interacting with Observation resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "based-on", - "type": "reference" - }, - { - "name": "category", - "type": "token" - }, - { - "name": "code", - "type": "token" - }, - { - "name": "component-code", - "type": "token" - }, - { - "name": "data-absent-reason", - "type": "token" - }, - { - "name": "date", - "type": "date" - }, - { - "name": "focus", - "type": "reference" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "subject", - "type": "reference" - }, - { - "name": "performer", - "type": "reference" - }, - { - "name": "specimen", - "type": "reference" - }, - { - "name": "value-string", - "type": "string" - }, - { - "name": "status", - "type": "token" - } - ] - }, - { - "type": "Patient", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient", - "documentation": "Endpoints for interacting with Patient resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "address", - "type": "string" - }, - { - "name": "birthdate", - "type": "date" - }, - { - "name": "death-date", - "type": "token" - }, - { - "name": "gender", - "type": "token" - }, - { - "name": "general-practitioner", - "type": "reference" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "link", - "type": "reference" - }, - { - "name": "name", - "type": "string" - }, - { - "name": "organization", - "type": "reference" - }, - { - "name": "telecom", - "type": "token" - } - ] - }, - { - "type": "Consent", - "profile": "http://hl7.org/fhir/StructureDefinition/Consent", - "documentation": "Endpoints for interacting with Consent resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "action", - "type": "token" - }, - { - "name": "actor", - "type": "reference" - }, - { - "name": "category", - "type": "token" - }, - { - "name": "consentor", - "type": "reference" - }, - { - "name": "identifier", - "type": "token" - }, - { - "name": "organization", - "type": "reference" - }, - { - "name": "patient", - "type": "reference" - }, - { - "name": "period", - "type": "date" - } - ] - }, - { - "type": "Condition", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Condition", - "documentation": "Endpoints for interacting with Condition resources", - "interaction": [ - { - "code": "read" - }, - { - "code": "vread" - }, - { - "code": "update" - }, - { - "code": "patch" - }, - { - "code": "delete" - }, - { - "code": "history-instance" - }, - { - "code": "create" - }, - { - "code": "search-type" - } - ], - "versioning": "versioned", - "readHistory": true, - "conditionalCreate": true, - "referencePolicy": [ - "resolves" - ], - "searchParam": [ - { - "name": "asserter", - "type": "reference" - }, - { - "name": "category", - "type": "token" - }, - { - "name": "clinical-status", - "type": "token" - }, - { - "name": "code", - "type": "token" - 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"code": "delete" + }, + { + "code": "history-instance" + }, + { + "code": "create" + }, + { + "code": "search-type" + } + ], + "versioning": "versioned", + "readHistory": true, + "conditionalCreate": true, + "referencePolicy": [ + "resolves" + ], + "searchParam": [ + { + "name": "identifier", + "type": "token" + }, + { + "name": "location", + "type": "token" + }, + { + "name": "morphology", + "type": "token" + }, + { + "name": "patient", + "type": "reference" + } + ] + }, + { + "type": "Provenance", + "profile": "http://hl7.org/fhir/StructureDefinition/Provenance", + "documentation": "For searching stored Provenance resources", + "interaction": [ + { + "code": "read" + }, + { + "code": "search-type" + } + ], + "searchParam": [ + { + "name": "agent", + "type": "reference" + }, + { + "name": "entity", + "type": "reference" + }, + { + "name": "target", + "type": "reference" + }, + { + "name": "recorded", + "type": "date" + } + ] + }, + { + "type": "DocumentReference", + "profile": "http://hl7.org/fhir/StructureDefinition/DocumentReference", + "documentation": "Endpoints for interacting with DocumentReference resources", + "interaction": [ + { + "code": "read" + }, + { + "code": "vread" + }, + { + "code": "update" + }, + { + "code": "patch" + }, + { + "code": "delete" + }, + { + "code": "history-instance" + }, + { + "code": "create" + }, + { + "code": "search-type" + } + ], + "versioning": "versioned", + "readHistory": true, + "conditionalCreate": true, + "referencePolicy": [ + "resolves" + ], + "searchParam": [ + { + "name": "date", + "type": "date" + }, + { + "name": "subject", + "type": "reference" + } + ] + }, + { + "type": "Composition", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Composition", + "documentation": "For validation of Composition resources and allowing searches via chaining from the Bundle endpoint", + "interaction": [ + { + "code": "search-type" + } + ], + "searchParam": [ + { + "name": "type", + "type": "token" + }, + { + "name": "subject", + "type": "reference" + }, + { + "name": "entry", + "type": "reference" + }, + { + "name": "date", + "type": "date" + } + ] + } + ] + } + ] } \ No newline at end of file From 7dcc67d5badd4d670ae4b87699c7bcb55fe6824c Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 9 Jan 2025 17:14:20 +0000 Subject: [PATCH 16/21] Update Package.json file Update Package.json file --- fhirpkg.lock.json | 7 ++++++- package.json | 5 ++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 31399d1d..cf246c4a 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -2,7 +2,12 @@ "updated": "2024-05-16T10:18:19.8963748+01:00", "dependencies": { "fhir.r4.ukcore.stu3.currentbuild": "0.0.17-pre-release", - "hl7.fhir.r4.core": "4.0.1" + "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", + "hl7.terminology.r4": "5.3.0", + "hl7.fhir.uv.extensions.r4": "1.0.0" }, "missing": {} } + + diff --git a/package.json b/package.json index 0adb71d4..b88c24e4 100644 --- a/package.json +++ b/package.json @@ -8,6 +8,9 @@ "jurisdiction": "urn:iso:std:iso:3166:-2:GB-ENG", "dependencies": { "fhir.r4.ukcore.stu3.currentbuild": "0.0.17-pre-release", - "hl7.fhir.r4.core": "4.0.1" + "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot" } } + + From e0f36d5cae6ed891345b4c060294603eeb4f4331 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 16 Jan 2025 11:28:03 +0000 Subject: [PATCH 17/21] Remove Duplicate NamingSystem Remove NamingSystem/England-GenomicTestPanelCodes.json --- .../England-GenomicTestPanelCodes.json | 43 ------------------- 1 file changed, 43 deletions(-) delete mode 100644 NamingSystem/England-GenomicTestPanelCodes.json diff --git a/NamingSystem/England-GenomicTestPanelCodes.json b/NamingSystem/England-GenomicTestPanelCodes.json deleted file mode 100644 index a7cfb037..00000000 --- a/NamingSystem/England-GenomicTestPanelCodes.json +++ /dev/null @@ -1,43 +0,0 @@ -{ - "resourceType": "NamingSystem", - "id": "England-GenomicTestPanelCodes", - "name": "EnglandGenomicTestPanelCodes", - "status": "draft", - "kind": "codesystem", - "date": "2023-05-23", - "publisher": "NHS England", - "contact": [ - { - "name": "NHS England", - "telecom": [ - { - "system": "email", - "value": "interoperabilityteam@nhs.net", - "use": "work", - "rank": 1 - } - ] - }, - { - "name": "NHS Genomic Medicine Service", - "telecom": [ - { - "system": "email", - "value": "england.genomics@nhs.net", - "use": "work", - "rank": 1 - } - ] - } - ], - "responsible": "NHS Genomic Interop Programme", - "description": "NamingSystem for Genomic Test Panel Codes", - "usage": "Used to define the system for Genomic Test Panel codes within ServiceRequest resources", - "uniqueId": [ - { - "type": "uri", - "value": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestPanelCodes", - "preferred": true - } - ] -} \ No newline at end of file From f51f56fa7ef77fbf0cfc9555d757a020066f59ac Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Mon, 20 Jan 2025 18:20:08 +0000 Subject: [PATCH 18/21] Solving Feedback Issues Update DiagnosticReport\DiagnosticReport-GenomicReport-VariantAssessment. --- ...rderFormUpdated-FetalScenario-Example.json | 0 ...eport-GenomicReport-VariantAssessment.json | 30 +++++++----- ...eference-StructureDataCapture-Example.json | 48 +++++++++++++++++++ ...vation-GenomicImplication-Therapeutic.json | 4 +- 4 files changed, 69 insertions(+), 13 deletions(-) rename {ServiceRequest => Bundle}/Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example.json (100%) create mode 100644 DocumentReference/DocumentReference-StructureDataCapture-Example.json diff --git a/ServiceRequest/Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example.json b/Bundle/Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example.json similarity index 100% rename from ServiceRequest/Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example.json rename to Bundle/Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example.json diff --git a/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json index 734f1937..c22cc5d2 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json +++ b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json @@ -17,18 +17,16 @@ { "url": "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact", "valueRelatedArtifact": { - "type": "citation", - "display": "Johnson et al 2012 (PMID22740598)" - } - + "type": "citation", + "display": "Johnson et al 2012 (PMID22740598)" + } }, { "url": "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact", "valueRelatedArtifact": { - "type": "citation", - "display": "Foley et al 2014 (PMID22740598)" - } - + "type": "citation", + "display": "Foley et al 2014 (PMID22740598)" + } }, { "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note", @@ -46,7 +44,7 @@ } } ], - "text": "This test was developed and its performance determined by this laboratory. It has not been cleared or approved by UK Food and Drug Administration.\nSince FDA Approval is not required for clinical use of this test, this laboratory has established and validated the test's accuracy and precision,\npursuant to the requirement of CLIA '88. This laboratory is licensed and/or accredited under CLIA and CAP (CAP# xxxxxxx / CLIA# xxxxxxxxxx)." + "text": "Proband whole genome sequencing by the 100,000 Genomics Project with analysis of the PanelApp Paediatric motor neuronopathies (version 1.6) gene panel followed by in-house Sanger sequencing confirmation. Please note that the sensitivity of this test is limited by the types of detectable pathogenic variants, regions of low read depth coverage and incomplete ascertainment of disease-gene associations. Further information including read depth coverage is available on request. *Variants are classified using the ACMG/AMP guidelines (Richards et al 2015 PMID25741868)." } } ], @@ -77,8 +75,8 @@ "subject": { "reference": "Patient/Patient-PheobeSmitham-Example" }, - "effectiveDateTime": "2023-09-16T00:00:00-05:00", - "issued": "2023-10-16T00:00:00-05:00", + "effectiveDateTime": "2023-10-16T00:00:00-05:00", + "issued": "2023-09-16T00:00:00-05:00", "performer": [ { "identifier": { @@ -107,5 +105,15 @@ } ] } + ], + "presentedForm": [ + { + "contentType": "application/pdf", + "language": "en-GB", + "url": "https://cts5j3.axshare.com/?id=mhxwul&p=final_report_issued_test_complete&g=1", + "size": 43272, + "title": "Genomic Report for Pheobe Smitham", + "creation": "2023-10-16" + } ] } \ No newline at end of file diff --git a/DocumentReference/DocumentReference-StructureDataCapture-Example.json b/DocumentReference/DocumentReference-StructureDataCapture-Example.json new file mode 100644 index 00000000..a59c61b9 --- /dev/null +++ b/DocumentReference/DocumentReference-StructureDataCapture-Example.json @@ -0,0 +1,48 @@ +{ + "resourceType": "DocumentReference", + "id": "DocumentReference-StructureDataCapture-Example", + "status": "current", + "docStatus": "final", + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307539" + } + }, + "date": "2023-10-16T09:45:00Z", + "author": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "R0A" + } + } + ], + "description": "Phenotype Report", + "content": [ + { + "attachment": { + "contentType": "application/json", + "url": "drs://drs.genomicsengland.nhs.uk/ga4gh/drs/v1/objects/42375e7d-071c-4eb3-b1c8-cec11e245cf0", + "title": "-Structure Data Capture JSON report" + } + } + ], + "context": { + "related": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + }, + { + "reference": "Specimen/Specimen-PheobeSmitham-Example" + }, + { + "reference": "Specimen/Specimen-PheobeSmithamFather-Example" + }, + { + "reference": "Specimen/Specimen-PheobeSmithamMother-Example" + } + ] + } +} \ No newline at end of file diff --git a/Observation/Observation-GenomicImplication-Therapeutic.json b/Observation/Observation-GenomicImplication-Therapeutic.json index 14be8f5e..fcea1fb4 100644 --- a/Observation/Observation-GenomicImplication-Therapeutic.json +++ b/Observation/Observation-GenomicImplication-Therapeutic.json @@ -65,8 +65,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6677-4", - "display": "Responsive" + "code": "LA9661-5", + "display": "Presumed responsive" } ] } From f02911a0bac61d83eb35e1295e956467ca221e4d Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Tue, 21 Jan 2025 19:31:09 +0000 Subject: [PATCH 19/21] Resolving Feedback Issues Added recommended components to OBS + update Task & DR Resources --- ...eport-GenomicReport-VariantAssessment.json | 5 ++ ...ation-GenomicsVariantSLC52A2-Example.json} | 81 ++++++++++++++----- ...-GenomicReport-FollowupRecommendation.json | 64 +++++++++++---- 3 files changed, 111 insertions(+), 39 deletions(-) rename Observation/{Observation-GenomicsVariant-SLC52A2.json => Observation-GenomicsVariantSLC52A2-Example.json} (73%) diff --git a/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json index c22cc5d2..4f223b87 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json +++ b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json @@ -102,6 +102,11 @@ "system": "http://loinc.org", "code": "LA6576-8", "display": "Positive" + }, + { + "system": "http://snomed.info/sct", + "code": "699866005", + "display": "Brown-Vialetto-Van Laere syndrome" } ] } diff --git a/Observation/Observation-GenomicsVariant-SLC52A2.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json similarity index 73% rename from Observation/Observation-GenomicsVariant-SLC52A2.json rename to Observation/Observation-GenomicsVariantSLC52A2-Example.json index 9a3a3510..1796fedf 100644 --- a/Observation/Observation-GenomicsVariant-SLC52A2.json +++ b/Observation/Observation-GenomicsVariantSLC52A2-Example.json @@ -1,6 +1,6 @@ { "resourceType": "Observation", - "id": "Observation-GenomicsVariant-SLC52A2", + "id": "Observation-GenomicsVariantSLC52A2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -35,11 +35,6 @@ { "system": "http://loinc.org", "code": "69548-6" - }, - { - "system": "http://snomed.info/sct", - "code": "699866005", - "display": "Brown-Vialetto-Van Laere syndrome" } ] }, @@ -82,17 +77,16 @@ "coding": [ { "system": "http://loinc.org", - "code": "48018-6" + "code": "48004-6" } - ], - "text": "SLC52A2" + ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/", - "code": "HGNC:30224", - "display": "SLC52A2" + "system": "https://hgvs-nomenclature.org/stable/", + "code": "NM_024531.4:c.9163>A p.(Gly306Arg)", + "display": "NM_024531.4:c.9163>A p.(Gly306Arg)" } ] } @@ -102,16 +96,35 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5" + "code": "81290-9" } ] }, "valueCodeableConcept": { + "coding": [ + { + "system": "https://hgvs-nomenclature.org/stable/", + "code": "Chr8:g.1455840683>A", + "display": "Chr8:g.1455840683>A" + } + ] + } + }, + { + "code": { "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "81252-9" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.sequenceontology.org", + "code": "SO:0001583", + "display": "missense_variant" } ] } @@ -121,7 +134,26 @@ "coding": [ { "system": "http://loinc.org", - "code": "94186-4" + "code": "48018-6" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.genenames.org/", + "code": "HGNC:30224", + "display": "SLC52A2" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53034-5" } ] }, @@ -129,8 +161,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA4489-6", - "display": "Unknown" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -140,12 +172,18 @@ "coding": [ { "system": "http://loinc.org", - "code": "48001-2" + "code": "94186-4" } ] }, "valueCodeableConcept": { - "text": "Biallelic Pathogenic:SLC52A2 missense variant" + "coding": [ + { + "system": "http://loinc.org", + "code": "LA4489-6", + "display": "Unknown" + } + ] } }, { @@ -164,8 +202,7 @@ "code": "LA6683-2", "display": "Germline" } - ], - "text": "Pathogenic" + ] } } ] diff --git a/Task/Task-GenomicReport-FollowupRecommendation.json b/Task/Task-GenomicReport-FollowupRecommendation.json index d25b1390..602a2f1e 100644 --- a/Task/Task-GenomicReport-FollowupRecommendation.json +++ b/Task/Task-GenomicReport-FollowupRecommendation.json @@ -1,27 +1,57 @@ { - "resourceType" : "Task", - "id" : "Task-GenomicReport-FollowupRecommendation", - "meta" : { - "profile" : [ + "resourceType": "Task", + "id": "Task-GenomicReport-FollowupRecommendation", + "meta": { + "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation" ] }, - "status" : "requested", - "intent" : "proposal", - "code" : { - "coding" : [ + "status": "requested", + "intent": "proposal", + "code": { + "coding": [ { - "system" : "http://loinc.org", - "code" : "LA14021-2", - "display" : "Confirmatory testing recommended" + "system": "http://loinc.org", + "code": "LA14021-2", + "display": "Confirmatory testing recommended" } ] }, - "description" : "Testing of Pheobe's parents is recommended (via referral to the clinical genetics service) in order to confirm that both are heterozygous carriers of the missense variant.", - "for" : { - "reference" : "Patient/Patient-PheobeSmitham-Example" + "description": "Testing of Pheobe's parents is recommended (via referral to the clinical genetics service) in order to confirm that both are heterozygous carriers of the missense variant.", + "for": { + "reference": "Patient/Patient-PheobeSmitham-Example" }, - "reasonReference" : { - "reference" : "Observation/Observation-GenomicImplication-Therapeutic" - } + "reasonReference": { + "reference": "Observation/Observation-GenomicImplication-Therapeutic" + }, + "input": [ + { + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "NFTH", + "display": "natural father" + } + ] + }, + "valueReference": { + "reference": "Patient/Patient-PheobeSmithamFather-Example" + } + }, + { + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "NMTH", + "display": "natural mother" + } + ] + }, + "valueReference": { + "reference": "Patient/Patient-PheobeSmithamMother-Example" + } + } + ] } \ No newline at end of file From 4aed50755730dc34db074d8e8860d80d54218c0e Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Wed, 22 Jan 2025 16:10:21 +0000 Subject: [PATCH 20/21] Update Observation-GenomicsVariantSLC52A2-Example.json Update and rename: Observation-GenomicsVariantSLC52A2-Example --- Observation/Observation-GenomicsVariantSLC52A2-Example.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json index 1796fedf..310f090e 100644 --- a/Observation/Observation-GenomicsVariantSLC52A2-Example.json +++ b/Observation/Observation-GenomicsVariantSLC52A2-Example.json @@ -84,7 +84,7 @@ "valueCodeableConcept": { "coding": [ { - "system": "https://hgvs-nomenclature.org/stable/", + "system": "http://varnomen.hgvs.org", "code": "NM_024531.4:c.9163>A p.(Gly306Arg)", "display": "NM_024531.4:c.9163>A p.(Gly306Arg)" } @@ -103,7 +103,7 @@ "valueCodeableConcept": { "coding": [ { - "system": "https://hgvs-nomenclature.org/stable/", + "system": "http://varnomen.hgvs.org", "code": "Chr8:g.1455840683>A", "display": "Chr8:g.1455840683>A" } From 173e90cb514004ad339c0d6042348222263f04c7 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Wed, 22 Jan 2025 16:32:39 +0000 Subject: [PATCH 21/21] Update Observation-GenomicsVariantSLC52A2-Example.json Update for Code\Systemhttp://varnomen.hgvs.org" --- Observation/Observation-GenomicsVariantSLC52A2-Example.json | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json index 310f090e..a5a6a2dc 100644 --- a/Observation/Observation-GenomicsVariantSLC52A2-Example.json +++ b/Observation/Observation-GenomicsVariantSLC52A2-Example.json @@ -85,8 +85,7 @@ "coding": [ { "system": "http://varnomen.hgvs.org", - "code": "NM_024531.4:c.9163>A p.(Gly306Arg)", - "display": "NM_024531.4:c.9163>A p.(Gly306Arg)" + "code": "NM_024531.4:c.9163>A p.(Gly306Arg)" } ] } @@ -104,8 +103,7 @@ "coding": [ { "system": "http://varnomen.hgvs.org", - "code": "Chr8:g.1455840683>A", - "display": "Chr8:g.1455840683>A" + "code": "Chr8:g.1455840683>A" } ] }