From f25751dd60c723100f1b8fbe3b171e4ea8c8803b Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 26 Nov 2025 16:12:30 +0000 Subject: [PATCH 1/4] [IOPS-3549] CapabilityStatement for DGTS --- .../CapabilityStatement-DGTS-application.json | 130 ++++++++++++++++++ 1 file changed, 130 insertions(+) create mode 100644 CapabilityStatement/CapabilityStatement-DGTS-application.json diff --git a/CapabilityStatement/CapabilityStatement-DGTS-application.json b/CapabilityStatement/CapabilityStatement-DGTS-application.json new file mode 100644 index 0000000..fcaff16 --- /dev/null +++ b/CapabilityStatement/CapabilityStatement-DGTS-application.json @@ -0,0 +1,130 @@ +{ + "resourceType": "CapabilityStatement", + "id": "CapabilityStatement-DGTS-application", + "url": "https://fhir.nhs.uk/CapabilityStatement/DGTS-application", + "version": "0.1.0", + "name": "CapabilityStatementDGTSApplication", + "status": "draft", + "date": "2025-11-26T00:00:00+00:00", + "publisher": "NHS England", + "description": "Sample server capability for the Digital Genomic Test Services API", + "kind": "instance", + "implementationGuide": [ + "https://simplifier.net/guide/fhir-genomics-implementation-guide" + ], + "fhirVersion": "4.0.1", + "format": [ + "application/fhir+json" + ], + "implementation": { + "description": "Exemplar CapabilityStatement for the GMS DGTS FHIR API" + }, + "rest": [ + { + "mode": "server", + "documentation": "RESTful endpoints supported by the DGTS FHIR API", + "resource": [ + { + "type": "PlanDefinition", + "profile": "http://hl7.org/fhir/StructureDefinition/PlanDefinition", + "documentation": "For searching DGTS Test Packages", + "interaction": [ + { + "code": "read" + }, + { + "code": "search-type" + } + ], + "searchParam": [ + { + "name": "context", + "type": "token" + }, + { + "name": "title", + "type": "string" + }, + { + "name": "url", + "type": "uri" + }, + { + "name": "version", + "type": "token" + } + ] + }, + { + "type": "ActivityDefinition", + "profile": "http://hl7.org/fhir/StructureDefinition/ActivityDefinition", + "documentation": "For searching DGTS Genomic Test", + "interaction": [ + { + "code": "read" + }, + { + "code": "search-type" + } + ], + "searchParam": [ + { + "name": "composed-of", + "type": "reference" + }, + { + "name": "context", + "type": "token" + }, + { + "name": "identifier", + "type": "token" + }, + { + "name": "title", + "type": "string" + }, + { + "name": "status", + "type": "token" + }, + { + "name": "url", + "type": "uri" + }, + { + "name": "version", + "type": "token" + } + ], + "operation": [ + { + "name": "$data-requirements" + "definition": "http://hl7.org/fhir/OperationDefinition/ActivityDefinition-data-requirements" + } + ] + }, + { + "type": "Library", + "profile": "http://hl7.org/fhir/StructureDefinition/Library", + "documentation": "Data requirements for DGTS Genomic Tests", + "interaction": [ + { + "code": "read" + } + ] + }, + { + "type": "SpecimenDefinition", + "profile": "http://hl7.org/fhir/StructureDefinition/SpecimenDefinition", + "documentation": "Specimen requirements for DGTS Genomic Tests", + "interaction": [ + { + "code": "read" + } + ] + } + ] + } + ] +} \ No newline at end of file From ac0c419ce06980df05f91b3016c7fd59db79005b Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 26 Nov 2025 17:36:56 +0000 Subject: [PATCH 2/4] [IOPS-3549] Examples for DGTS --- .../DGTS-ActivityDefinition-Example.json | 53 ++++++++ Library/DGTS-Library-Example.json | 39 ++++++ .../DGTS-PlanDefinition-Example.json | 118 ++++++++++++++++++ .../DGTS-SpecimenDefinition-Example.json | 39 ++++++ 4 files changed, 249 insertions(+) create mode 100644 ActivityDefinition/DGTS-ActivityDefinition-Example.json create mode 100644 Library/DGTS-Library-Example.json create mode 100644 PlanDefinition/DGTS-PlanDefinition-Example.json create mode 100644 SpecimenDefinition/DGTS-SpecimenDefinition-Example.json diff --git a/ActivityDefinition/DGTS-ActivityDefinition-Example.json b/ActivityDefinition/DGTS-ActivityDefinition-Example.json new file mode 100644 index 0000000..a8ad9bf --- /dev/null +++ b/ActivityDefinition/DGTS-ActivityDefinition-Example.json @@ -0,0 +1,53 @@ +{ + "resourceType": "ActivityDefinition", + "id": "DGTS-ActivityDefinition-Example", + "url": "http://fhir.nhs.uk/ActivityDefinition/GT1", + "identifier": [ + { + "system": "http://fhir.nhs.uk/Id/Genomics-DGTS", + "value": "GT1" + } + ], + "version": "1.0", + "status": "active", + "experimental": false, + "useContext": [ + { + "code": { + "code": "focus" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "diagnostic", + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics" + } + ] + } + } + ], + "code": { + "coding": [ + { + "code": "targeted-variant-analysis", + "system": "http://hl7.org/fhir/genomicstudy-methodtype" + } + ] + }, + "library": [ + "http://fhir.nhs.uk/Library/GT1" + ], + "specimenRequirement": [ + { + "reference": "SpecimenDefinition/DGTS-SpecimenDefinition-Example" + } + ], + "relatedArtifact": [ + { + "type": "composed-of", + "url": "https://panelapp.genomicsengland.co.uk/panels/1313", + "label": "Carney complex", + "display": "GMS Rare Disease" + } + ] +} \ No newline at end of file diff --git a/Library/DGTS-Library-Example.json b/Library/DGTS-Library-Example.json new file mode 100644 index 0000000..4e976b6 --- /dev/null +++ b/Library/DGTS-Library-Example.json @@ -0,0 +1,39 @@ +{ + "resourceType": "Library", + "id": "DGTS-Library-Example", + "url": "http://fhir.nhs.uk/Library/GT1", + "type": { + "coding": [ + { + "code": "module-definition" + } + ] + }, + "status": "active", + "parameter": [ + { + "name": "additional_panels_available", + "use": "in", + "max": "0" + "type": "Coding" + }, + { + "name": "target_disease_required", + "use": "in", + "max": "0", + "type": "Coding" + }, + { + "name": "target_gene_required", + "use": "in", + "max": "0", + "type": "Coding" + }, + { + "name": "target_variant_required", + "use": "in", + "max": "0", + "type": "Coding" + } + ] +} \ No newline at end of file diff --git a/PlanDefinition/DGTS-PlanDefinition-Example.json b/PlanDefinition/DGTS-PlanDefinition-Example.json new file mode 100644 index 0000000..2b373ba --- /dev/null +++ b/PlanDefinition/DGTS-PlanDefinition-Example.json @@ -0,0 +1,118 @@ +{ + "resourceType": "PlanDefinition", + "id": "DGTS-PlanDefinition-Example", + "url": "http://fhir.nhs.uk/PlanDefinition/TP231", + "identifier": [ + { + "system": "http://fhir.nhs.uk/Id/Genomics-DGTS-TestPackage", + "value": "TP231" + } + ], + "title": "Angelman syndrome" + "status": "active", + "experimental": false, + "version": "1.0", + "useContext": [ + { + "code": { + "code": "user", + "system": "http://terminology.hl7.org/CodeSystem/usage-context-type" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "400", + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-PracticeSettingCode", + "display": "Neurology" + + } + ] + } + }, + { + "code": { + "code": "user", + "system": "http://terminology.hl7.org/CodeSystem/usage-context-type" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "420", + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-PracticeSettingCode", + "display": "Paediatrics" + + } + ] + } + }, + { + "code": { + "code": "user", + "system": "http://terminology.hl7.org/CodeSystem/usage-context-type" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "311", + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-PracticeSettingCode", + "display": "Clinical Genetics" + + } + ] + } + }, + { + "code": { + "code": "focus", + "system": "http://terminology.hl7.org/CodeSystem/usage-context-type" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "diagnostic", + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics" + } + ] + } + } + ], + "goal": [ + { + "description": { + "coding": [ + { + "code": "rare-disease-non-wgs", + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory", + "display": "Rare Disease - Non-WGS" + } + ] + } + } + ], + "action": [ + { + "definitionCanonical": "http://fhir.nhs.uk/ActivityDefinition/GT1" + }, + { + "definitionCanonical": "http://fhir.nhs.uk/ActivityDefinition/GT36" + }, + { + "definitionCanonical": "http://fhir.nhs.uk/ActivityDefinition/GT103" + }, + { + "definitionCanonical": "http://fhir.nhs.uk/ActivityDefinition/GT417" + }, + { + "definitionCanonical": "http://fhir.nhs.uk/ActivityDefinition/GT732" + }, + { + "definitionCanonical": "http://fhir.nhs.uk/ActivityDefinition/GT858" + }, + { + "definitionCanonical": "http://fhir.nhs.uk/ActivityDefinition/GT897" + }, + { + "definitionCanonical": "http://fhir.nhs.uk/ActivityDefinition/GT1124" + } + ] +} \ No newline at end of file diff --git a/SpecimenDefinition/DGTS-SpecimenDefinition-Example.json b/SpecimenDefinition/DGTS-SpecimenDefinition-Example.json new file mode 100644 index 0000000..9548c0e --- /dev/null +++ b/SpecimenDefinition/DGTS-SpecimenDefinition-Example.json @@ -0,0 +1,39 @@ +{ + "resourceType": "SpecimenDefinition", + "id": "DGTS-SpecimenDefinition-Example", + "typeCollected": { + "coding": [ + { + "code": "germline", + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory" + } + ] + }, + "typeTested": [ + { + "type": { + "coding": [ + { + "code": "119297000", + "system": "http://snomed.info/sct", + "display": "Blood specimen" + } + ] + }, + "preference": "preferred", + "container": { + "additive": [ + { + "additiveCodeableConcept" [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0371", + "code": "EDTK15", + "display": "Potassium/K EDTA 15%" + } + ] + } + ] + } + } + ] +} \ No newline at end of file From d26474321d231fe3650d7eda679648c54983fae3 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 26 Nov 2025 17:38:53 +0000 Subject: [PATCH 3/4] Fixed missing comma --- PlanDefinition/DGTS-PlanDefinition-Example.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PlanDefinition/DGTS-PlanDefinition-Example.json b/PlanDefinition/DGTS-PlanDefinition-Example.json index 2b373ba..8854b9d 100644 --- a/PlanDefinition/DGTS-PlanDefinition-Example.json +++ b/PlanDefinition/DGTS-PlanDefinition-Example.json @@ -8,7 +8,7 @@ "value": "TP231" } ], - "title": "Angelman syndrome" + "title": "Angelman syndrome", "status": "active", "experimental": false, "version": "1.0", From 51ded15ca551d644c5d9744d97d5e8706b613954 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 26 Nov 2025 17:49:57 +0000 Subject: [PATCH 4/4] Addition of missing title for test --- .../DGTS-ActivityDefinition-Example.json | 103 +++++++++--------- 1 file changed, 52 insertions(+), 51 deletions(-) diff --git a/ActivityDefinition/DGTS-ActivityDefinition-Example.json b/ActivityDefinition/DGTS-ActivityDefinition-Example.json index a8ad9bf..373d3ec 100644 --- a/ActivityDefinition/DGTS-ActivityDefinition-Example.json +++ b/ActivityDefinition/DGTS-ActivityDefinition-Example.json @@ -1,53 +1,54 @@ { - "resourceType": "ActivityDefinition", - "id": "DGTS-ActivityDefinition-Example", - "url": "http://fhir.nhs.uk/ActivityDefinition/GT1", - "identifier": [ - { - "system": "http://fhir.nhs.uk/Id/Genomics-DGTS", - "value": "GT1" - } - ], - "version": "1.0", - "status": "active", - "experimental": false, - "useContext": [ - { - "code": { - "code": "focus" - }, - "valueCodeableConcept": { - "coding": [ - { - "code": "diagnostic", - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics" - } - ] - } - } - ], - "code": { - "coding": [ - { - "code": "targeted-variant-analysis", - "system": "http://hl7.org/fhir/genomicstudy-methodtype" - } - ] - }, - "library": [ - "http://fhir.nhs.uk/Library/GT1" - ], - "specimenRequirement": [ - { - "reference": "SpecimenDefinition/DGTS-SpecimenDefinition-Example" - } - ], - "relatedArtifact": [ - { - "type": "composed-of", - "url": "https://panelapp.genomicsengland.co.uk/panels/1313", - "label": "Carney complex", - "display": "GMS Rare Disease" - } - ] + "resourceType": "ActivityDefinition", + "id": "DGTS-ActivityDefinition-Example", + "url": "http://fhir.nhs.uk/ActivityDefinition/GT1", + "identifier": [ + { + "system": "http://fhir.nhs.uk/Id/Genomics-DGTS", + "value": "GT1" + } + ], + "title": "15q11 critical region (AS/PWS) - MLPA or equivalent", + "version": "1.0", + "status": "active", + "experimental": false, + "useContext": [ + { + "code": { + "code": "focus" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "diagnostic", + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics" + } + ] + } + } + ], + "code": { + "coding": [ + { + "code": "targeted-variant-analysis", + "system": "http://hl7.org/fhir/genomicstudy-methodtype" + } + ] + }, + "library": [ + "http://fhir.nhs.uk/Library/GT1" + ], + "specimenRequirement": [ + { + "reference": "SpecimenDefinition/DGTS-SpecimenDefinition-Example" + } + ], + "relatedArtifact": [ + { + "type": "composed-of", + "url": "https://panelapp.genomicsengland.co.uk/panels/1313", + "label": "Carney complex", + "display": "GMS Rare Disease" + } + ] } \ No newline at end of file