From af2f3bcb1bbdd9b033ac0a19443dbb429fc72c62 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Mon, 9 Feb 2026 18:01:53 +0000 Subject: [PATCH 1/3] Create and Update Term Assets Update ValueSet-Genomics-reason-for-testing --- .../CodeSystem-Genomics-cancer-testing.json | 77 +++++ .../CodeSystem-Genomics-clinical-utility.json | 41 +++ ...odeSystem-Genomics-reason-for-testing.json | 181 ++++++------ ...ystem-Genomics-test-associationReason.json | 53 ++++ .../ValueSet-Genomics-reason-for-testing.json | 279 ++++++++++++++++-- 5 files changed, 514 insertions(+), 117 deletions(-) create mode 100644 CodeSystem/CodeSystem-Genomics-cancer-testing.json create mode 100644 CodeSystem/CodeSystem-Genomics-clinical-utility.json create mode 100644 CodeSystem/CodeSystem-Genomics-test-associationReason.json diff --git a/CodeSystem/CodeSystem-Genomics-cancer-testing.json b/CodeSystem/CodeSystem-Genomics-cancer-testing.json new file mode 100644 index 0000000..8d2024b --- /dev/null +++ b/CodeSystem/CodeSystem-Genomics-cancer-testing.json @@ -0,0 +1,77 @@ +{ + "resourceType": "CodeSystem", + "id": "cancer-testing-genomics", + "url": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "version": "0.1.0", + "name": "CancerTestingGenomics", + "title": "Cancer Testing Genomics", + "status": "draft", + "date": "2026-02-06T00:00:00.000Z", + "publisher": "NHS England", + "contact": [ + { + "name": "NHS England", + "telecom": [ + { + "system": "email", + "value": "interoperabilityteam@nhs.net" + } + ] + } + ], + "description": "CodeSystem used to identify Genomic test requested based on cancer suspicion/treatment.", + "copyright": "Copyright © 2026+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", + "caseSensitive": true, + "content": "complete", + "count": 12, + "concept": [ + { + "code": "sample-storage", + "display": "Sample storage" + }, + { + "code": "diagnostic", + "display": "Diagnostic" + }, + { + "code": "differential-diagnosis", + "display": "Differential diagnosis" + }, + { + "code": "prognostic", + "display": "Prognostic" + }, + { + "code": "treatment-determining", + "display": "Treatment determining" + }, + { + "code": "disease-monitoring", + "display": "Disease monitoring" + }, + { + "code": "relapse-recurrence", + "display": "Relapse or recurrence" + }, + { + "code": "remission", + "display": "Remission" + }, + { + "code": "transformation", + "display": "Transformation" + }, + { + "code": "research-trial-eligibility", + "display": "Research or trial eligibility" + }, + { + "code": "pharmacogenomics", + "display": "Pharmacogenomics" + }, + { + "code": "other", + "display": "Other" + } + ] +} \ No newline at end of file diff --git a/CodeSystem/CodeSystem-Genomics-clinical-utility.json b/CodeSystem/CodeSystem-Genomics-clinical-utility.json new file mode 100644 index 0000000..7900765 --- /dev/null +++ b/CodeSystem/CodeSystem-Genomics-clinical-utility.json @@ -0,0 +1,41 @@ +{ + "resourceType": "CodeSystem", + "id": "clinical-utility-genomics", + "url": "https://fhir.nhs.uk/CodeSystem/clinical-utility-genomics", + "version": "0.1.0", + "name": "ClinicalUtilityGenomics", + "title": "Clinical Utility Genomics", + "status": "draft", + "date": "2026-02-06T00:00:00.000Z", + "publisher": "NHS England", + "contact": [ + { + "name": "NHS England", + "telecom": [ + { + "system": "email", + "value": "interoperabilityteam@nhs.net" + } + ] + } + ], + "description": "CodeSystem used for classifying clinical benefit of requesting genomic test for a patient", + "copyright": "Copyright © 2026+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", + "caseSensitive": true, + "content": "complete", + "count": 3, + "concept": [ + { + "code": "patient-management", + "display": "Patient management" + }, + { + "code": "reproductive-decision-making", + "display": "Reproductive decision making" + }, + { + "code": "unaffected-relatives-seeking-predictive-testing", + "display": "Unaffected relatives seeking predictive testing" + } + ] +} \ No newline at end of file diff --git a/CodeSystem/CodeSystem-Genomics-reason-for-testing.json b/CodeSystem/CodeSystem-Genomics-reason-for-testing.json index ef32cf1..cf55d72 100644 --- a/CodeSystem/CodeSystem-Genomics-reason-for-testing.json +++ b/CodeSystem/CodeSystem-Genomics-reason-for-testing.json @@ -1,100 +1,101 @@ { - "resourceType": "CodeSystem", - "id": "reasonfortesting-genomics", - "url": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "version": "0.2.0", - "name": "ReasonforTestingGenomics", - "title": "Reason for Testing Genomics", - "status": "draft", - "date": "2025-09-09T00:00:00.000Z", - "publisher": "NHS England", - "contact": [ + "resourceType": "CodeSystem", + "id": "reasonfortesting-genomics", + "url": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "version": "0.3.0", + "name": "ReasonforTestingGenomics", + "title": "Reason for Testing Genomics", + "status": "draft", + "date": "2026-02-09T00:00:00.000Z", + "publisher": "NHS England", + "contact": [ + { + "name": "NHS England", + "telecom": [ { - "name": "NHS England", - "telecom": [ - { - "system": "email", - "value": "interoperabilityteam@nhs.net" - } - ] + "system": "email", + "value": "interoperabilityteam@nhs.net" } - ], - "description": "A set of codes use to identify the reason for requesting a genomics test.This is intended to be used on ServiceRequest.category.", - "copyright": "Copyright © 2023+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", - "caseSensitive": true, - "content": "complete", - "concept": [ + ] + } + ], + "description": "A set of codes use to identify the reason for requesting a genomics test.This is intended to be used on ServiceRequest.category.", + "copyright": "Copyright © 2023+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", + "caseSensitive": true, + "content": "complete", + "count": 17, + "concept": [ + { + "code": "primary-test-request", + "display": "Primary Test Request", + "concept": [ { - "code": "primary-test-request", - "display": "Primary Test Request", - "concept": [ - { - "code": "carrier", - "display": "Carrier" - }, - { - "code": "diagnostic", - "display": "Diagnostic" - }, - { - "code": "disease-monitoring-mrdmechanism", - "display": "Disease Monitoring MRD CHIMERISM" - }, - { - "code": "dna-storage", - "display": "DNA Storage" - }, - { - "code": "follow-up", - "display": "Follow Up" - }, - { - "code": "predictive", - "display": "Predictive" - }, - { - "code": "relapse", - "display": "Relapse" - }, - { - "code": "staging-or-prognosis", - "display": "Staging or Prognosis" - }, - { - "code": "unknown", - "display": "Unknown" - } - ] + "code": "carrier", + "display": "Carrier" }, { - "code": "reanalysis-test-request", - "display": "Reanalysis Test Request", - "concept": [ - { - "code": "change-in-presentation", - "display": "Change In Presentation" - }, - { - "code": "newly-affected-family-member", - "display": "Newly Affected Family Member" - }, - { - "code": "new-pregnancy", - "display": "New Pregnancy" - }, - { - "code": "new-treatment-clinical-management", - "display": "New Treatment/Clinical Management" - }, - { - "code": "recently-deceased-to-inform-family", - "display": "Recently Deceased To Inform Family" - } - ] + "code": "diagnostic", + "display": "Diagnostic" }, { - "code": "other", - "display": "Other" + "code": "disease-monitoring-mrdmechanism", + "display": "Disease monitoring MRD CHIMERISM" + }, + { + "code": "dna-storage", + "display": "DNA storage" + }, + { + "code": "follow-up", + "display": "Follow up" + }, + { + "code": "predictive", + "display": "Predictive" + }, + { + "code": "relapse", + "display": "Relapse" + }, + { + "code": "staging-or-prognosis", + "display": "Staging or Prognosis" + }, + { + "code": "unknown", + "display": "Unknown" + } + ] + }, + { + "code": "reanalysis-test-request", + "display": "Reanalysis test request", + "concept": [ + { + "code": "change-in-presentation", + "display": "Change in presentation" + }, + { + "code": "newly-affected-family-member", + "display": "Newly affected family member" + }, + { + "code": "new-pregnancy", + "display": "New pregnancy" + }, + { + "code": "new-treatment-clinical-management", + "display": "New treatment/clinical management" + }, + { + "code": "recently-deceased-to-inform-family", + "display": "Recently deceased to Inform family" } - ] + ] + }, + { + "code": "other", + "display": "Other" + } + ] } \ No newline at end of file diff --git a/CodeSystem/CodeSystem-Genomics-test-associationReason.json b/CodeSystem/CodeSystem-Genomics-test-associationReason.json new file mode 100644 index 0000000..6f98d25 --- /dev/null +++ b/CodeSystem/CodeSystem-Genomics-test-associationReason.json @@ -0,0 +1,53 @@ +{ + "resourceType": "CodeSystem", + "id": "test-associationReason-genomics", + "url": "https://fhir.nhs.uk/CodeSystem/test-associationReason-genomics", + "version": "0.1.0", + "name": "TestAssociationReasonGenomics", + "title": "Test Association Reason Genomics", + "status": "draft", + "date": "2026-02-06T00:00:00.000Z", + "publisher": "NHS England", + "contact": [ + { + "name": "NHS England", + "telecom": [ + { + "system": "email", + "value": "interoperabilityteam@nhs.net" + } + ] + } + ], + "description": "CodeSystem used for specifying the purposes for linking a primary genomic test to a subsequent or related test.", + "copyright": "Copyright © 2026+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", + "caseSensitive": true, + "content": "complete", + "count": 6, + "concept": [ + { + "code": "reanalysis", + "display": "Re-analysis" + }, + { + "code": "reinterpretation", + "display": " Re-interpretation" + }, + { + "code": "retest", + "display": "Re-test" + }, + { + "code": "follow-on-test", + "display": "Follow on test" + }, + { + "code": "family-associated", + "display": "Family associated" + }, + { + "code": "germline-later", + "display": "Germline later" + } + ] +} \ No newline at end of file diff --git a/ValueSet/ValueSet-Genomics-reason-for-testing.json b/ValueSet/ValueSet-Genomics-reason-for-testing.json index dfe9d0f..b25a2d0 100644 --- a/ValueSet/ValueSet-Genomics-reason-for-testing.json +++ b/ValueSet/ValueSet-Genomics-reason-for-testing.json @@ -1,32 +1,257 @@ { - "resourceType": "ValueSet", - "id": "genomics-reasonfortesting", - "url": "https://fhir.nhs.uk/ValueSet/genomics-reasonfortesting", - "version": "0.2.0", - "name": "GenomicsReasonforTesting", - "title": "Genomics Reason for Testing", - "status": "draft", - "date": "2025-09-09T00:00:00.000Z", - "publisher": "NHS England", - "contact": [ + "resourceType": "ValueSet", + "id": "genomics-reasonfortesting", + "url": "https://fhir.nhs.uk/ValueSet/genomics-reasonfortesting", + "version": "0.3.0", + "name": "GenomicsReasonforTesting", + "title": "Genomics Reason for Testing", + "status": "draft", + "date": "2026-02-09T00:00:00.000Z", + "publisher": "NHS England", + "contact": [ + { + "name": "NHS England", + "telecom": [ { - "name": "NHS England", - "telecom": [ - { - "system": "email", - "value": "interoperabilityteam@nhs.net" - } - ] + "system": "email", + "value": "interoperabilityteam@nhs.net" } - ], - "description": "A ValueSet use to identify the reason for requesting a genomics test.", - "copyright": "Copyright © 2023+ NHS England Licensed under the Apache License, Version 2.0 (the \\\\\\\"License\\\\\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\\\\\"AS IS\\\\\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", - "compose": { - "include": [ - { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "version": "0.2.0" - } - ] + ] } + ], + "description": "A Composite ValueSet of reasons for requesting or linking genomics test.", + "copyright": "Copyright © 2023+ NHS England Licensed under the Apache License, Version 2.0 (the \\\\\\\"License\\\\\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\\\\\"AS IS\\\\\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", + "compose": { + "include": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "version": "0.3.0", + "filter": [ + { + "property": "concept", + "op": "is-a", + "value": "primary-test-request" + } + ] + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "version": "0.3.0", + "concept": [ + { + "code": "reanalysis-test-request", + "display": "Reanalysis Test Request" + }, + { + "code": "other", + "display": "Other" + } + ] + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "version": "0.1.0" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/clinical-utility-genomics", + "version": "0.1.0" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/test-associationReason-genomics", + "version": "0.1.0" + } + ] + }, + "expansion": { + "identifier": "urn:uuid:3f2a1b9c-2d75-45cc-8ea3-2e747e4b61d4", + "timestamp": "2026-02-09T00:00:00Z", + "total": 37, + "contains": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "carrier", + "display": "Carrier" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "diagnostic", + "display": "Diagnostic" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "disease-monitoring-mrdmechanism", + "display": "Disease monitoring MRD CHIMERISM" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "dna-storage", + "display": "DNA storage" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "follow-up", + "display": "Follow up" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "predictive", + "display": "Predictive" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "relapse", + "display": "Relapse" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "staging-or-prognosis", + "display": "Staging or Prognosis" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "unknown", + "display": "Unknown" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "reanalysis-test-request", + "display": "Reanalysis test request" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "change-in-presentation", + "display": "Change in presentation" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "newly-affected-family-member", + "display": "Newly affected family member" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "new-pregnancy", + "display": "New pregnancy" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "new-treatment-clinical-management", + "display": "New treatment/clinical management" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "recently-deceased-to-inform-family", + "display": "Recently deceased to inform family" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "other", + "display": "Other" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "code": "sample-storage", + "display": "Sample storage" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "code": "diagnostic", + "display": "Diagnostic" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "code": "differential-diagnosis", + "display": "Differential diagnosis" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "code": "prognostic", + "display": "Prognostic" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "code": "treatment-determining", + "display": "Treatment determining" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "code": "disease-monitoring", + "display": "Disease monitoring" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "code": "relapse-recurrence", + "display": "Relapse or recurrence" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "code": "remission", + "display": "Remission" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "code": "transformation", + "display": "Transformation" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "code": "research-trial-eligibility", + "display": "Research or trial eligibility" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "code": "pharmacogenomics", + "display": "Pharmacogenomics" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", + "code": "other", + "display": "Other" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/clinical-utility-genomics", + "code": "patient-management", + "display": "Patient management" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/clinical-utility-genomics", + "code": "reproductive-decision-making", + "display": "Reproductive decision making" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/clinical-utility-genomics", + "code": "unaffected-relatives-seeking-predictive-testing", + "display": "Unaffected relatives seeking predictive testing" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/test-associationReason-genomics", + "code": "reanalysis", + "display": "Re-analysis" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/test-associationReason-genomics", + "code": "reinterpretation", + "display": "Re-interpretation" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/test-associationReason-genomics", + "code": "retest", + "display": "Re-test" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/test-associationReason-genomics", + "code": "follow-on-test", + "display": "Follow on test" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/test-associationReason-genomics", + "code": "family-associated", + "display": "Family associated" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/test-associationReason-genomics", + "code": "germline-later", + "display": "Germline later" + } + ] + } } \ No newline at end of file From 200c10ea602abaecaf4400f08f9911197d81dae1 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Tue, 10 Feb 2026 12:04:12 +0000 Subject: [PATCH 2/3] Retire CodeSystem-Genomics-reason-for-testing Due to change in name and new code values define in MDS v1.0.5 --- ...deSystem-Genomics-rare-diseaseTesting.json | 65 +++++++++++ ...odeSystem-Genomics-reason-for-testing.json | 25 ++--- .../ValueSet-Genomics-reason-for-testing.json | 106 +++++------------- 3 files changed, 102 insertions(+), 94 deletions(-) create mode 100644 CodeSystem/CodeSystem-Genomics-rare-diseaseTesting.json diff --git a/CodeSystem/CodeSystem-Genomics-rare-diseaseTesting.json b/CodeSystem/CodeSystem-Genomics-rare-diseaseTesting.json new file mode 100644 index 0000000..ece4bcc --- /dev/null +++ b/CodeSystem/CodeSystem-Genomics-rare-diseaseTesting.json @@ -0,0 +1,65 @@ +{ + "resourceType": "CodeSystem", + "id": "rare-diseaseTesting-genomics", + "url": "https://fhir.nhs.uk/CodeSystem/rare-diseaseTesting-genomics", + "version": "0.1.0", + "name": "RareDiseaseTestingGenomics", + "title": "Rare Disease Testing Genomics", + "status": "draft", + "date": "2026-02-10T00:00:00.000Z", + "publisher": "NHS England", + "contact": [ + { + "name": "NHS England", + "telecom": [ + { + "system": "email", + "value": "interoperabilityteam@nhs.net" + } + ] + } + ], + "description": "CodeSystem used to identify Genomic test requested based on rare disease suspicion/treatment.", + "copyright": "Copyright © 2026+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", + "caseSensitive": true, + "content": "complete", + "count": 12, + "concept": [ + { + "code": "sample-storage", + "display": "Sample storage" + }, + { + "code": "diagnostic", + "display": "Diagnostic" + }, + { + "code": "carrier", + "display": "Carrier" + }, + { + "code": "predictive", + "display": "Predictive" + }, + { + "code": "prenatal-diagnosis", + "display": "Prenatal diagnosis" + }, + { + "code": "family-member-to-aid-interpretation", + "display": "Family member to aid interpretation of a relative's result/variant" + }, + { + "code": "reanalysis", + "display": "Reanalysis" + }, + { + "code": "pharmacogenomics", + "display": "Pharmacogenomics" + }, + { + "code": "other", + "display": "Other" + } + ] +} \ No newline at end of file diff --git a/CodeSystem/CodeSystem-Genomics-reason-for-testing.json b/CodeSystem/CodeSystem-Genomics-reason-for-testing.json index cf55d72..562ee2d 100644 --- a/CodeSystem/CodeSystem-Genomics-reason-for-testing.json +++ b/CodeSystem/CodeSystem-Genomics-reason-for-testing.json @@ -2,11 +2,11 @@ "resourceType": "CodeSystem", "id": "reasonfortesting-genomics", "url": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "version": "0.3.0", + "version": "0.2.0", "name": "ReasonforTestingGenomics", "title": "Reason for Testing Genomics", - "status": "draft", - "date": "2026-02-09T00:00:00.000Z", + "status": "retired", + "date": "2026-02-10T00:00:00.000Z", "publisher": "NHS England", "contact": [ { @@ -23,7 +23,6 @@ "copyright": "Copyright © 2023+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", "caseSensitive": true, "content": "complete", - "count": 17, "concept": [ { "code": "primary-test-request", @@ -39,15 +38,15 @@ }, { "code": "disease-monitoring-mrdmechanism", - "display": "Disease monitoring MRD CHIMERISM" + "display": "Disease Monitoring MRD CHIMERISM" }, { "code": "dna-storage", - "display": "DNA storage" + "display": "DNA Storage" }, { "code": "follow-up", - "display": "Follow up" + "display": "Follow Up" }, { "code": "predictive", @@ -69,27 +68,27 @@ }, { "code": "reanalysis-test-request", - "display": "Reanalysis test request", + "display": "Reanalysis Test Request", "concept": [ { "code": "change-in-presentation", - "display": "Change in presentation" + "display": "Change In Presentation" }, { "code": "newly-affected-family-member", - "display": "Newly affected family member" + "display": "Newly Affected Family Member" }, { "code": "new-pregnancy", - "display": "New pregnancy" + "display": "New Pregnancy" }, { "code": "new-treatment-clinical-management", - "display": "New treatment/clinical management" + "display": "New Treatment/Clinical Management" }, { "code": "recently-deceased-to-inform-family", - "display": "Recently deceased to Inform family" + "display": "Recently Deceased To Inform Family" } ] }, diff --git a/ValueSet/ValueSet-Genomics-reason-for-testing.json b/ValueSet/ValueSet-Genomics-reason-for-testing.json index b25a2d0..64433d4 100644 --- a/ValueSet/ValueSet-Genomics-reason-for-testing.json +++ b/ValueSet/ValueSet-Genomics-reason-for-testing.json @@ -24,29 +24,8 @@ "compose": { "include": [ { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "version": "0.3.0", - "filter": [ - { - "property": "concept", - "op": "is-a", - "value": "primary-test-request" - } - ] - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "version": "0.3.0", - "concept": [ - { - "code": "reanalysis-test-request", - "display": "Reanalysis Test Request" - }, - { - "code": "other", - "display": "Other" - } - ] + "system": "https://fhir.nhs.uk/CodeSystem/rare-diseaseTesting-genomics", + "version": "0.1.0" }, { "system": "https://fhir.nhs.uk/CodeSystem/cancer-testing-genomics", @@ -64,86 +43,51 @@ }, "expansion": { "identifier": "urn:uuid:3f2a1b9c-2d75-45cc-8ea3-2e747e4b61d4", - "timestamp": "2026-02-09T00:00:00Z", - "total": 37, + "timestamp": "2026-02-10T00:00:00Z", + "total": 30, "contains": [ { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "carrier", - "display": "Carrier" + "system": "https://fhir.nhs.uk/CodeSystem/rare-diseaseTesting-genomics", + "code": "sample-storage", + "display": "Sample storage" }, { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "system": "https://fhir.nhs.uk/CodeSystem/rare-diseaseTesting-genomics", "code": "diagnostic", "display": "Diagnostic" }, { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "disease-monitoring-mrdmechanism", - "display": "Disease monitoring MRD CHIMERISM" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "dna-storage", - "display": "DNA storage" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "follow-up", - "display": "Follow up" + "system": "https://fhir.nhs.uk/CodeSystem/rare-diseaseTesting-genomics", + "code": "carrier", + "display": "Carrier" }, { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "system": "https://fhir.nhs.uk/CodeSystem/rare-diseaseTesting-genomics", "code": "predictive", "display": "Predictive" }, { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "relapse", - "display": "Relapse" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "staging-or-prognosis", - "display": "Staging or Prognosis" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "unknown", - "display": "Unknown" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "reanalysis-test-request", - "display": "Reanalysis test request" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "change-in-presentation", - "display": "Change in presentation" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "newly-affected-family-member", - "display": "Newly affected family member" + "system": "https://fhir.nhs.uk/CodeSystem/rare-diseaseTesting-genomics", + "code": "prenatal-diagnosis", + "display": "Prenatal diagnosis" }, { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "new-pregnancy", - "display": "New pregnancy" + "system": "https://fhir.nhs.uk/CodeSystem/rare-diseaseTesting-genomics", + "code": "family-member-to-aid-interpretation", + "display": "Family member to aid interpretation of a relative's result/variant" }, { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "new-treatment-clinical-management", - "display": "New treatment/clinical management" + "system": "https://fhir.nhs.uk/CodeSystem/rare-diseaseTesting-genomics", + "code": "reanalysis", + "display": "Reanalysis" }, { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "recently-deceased-to-inform-family", - "display": "Recently deceased to inform family" + "system": "https://fhir.nhs.uk/CodeSystem/rare-diseaseTesting-genomics", + "code": "pharmacogenomics", + "display": "Pharmacogenomics" }, { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "system": "https://fhir.nhs.uk/CodeSystem/rare-diseaseTesting-genomics", "code": "other", "display": "Other" }, From 72aed8c636844f1b9bb15511778c36fafc14f4fd Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Tue, 10 Feb 2026 12:13:55 +0000 Subject: [PATCH 3/3] Update CodeSystem-Genomics-rare-diseaseTesting. Fixing errors on element total --- CodeSystem/CodeSystem-Genomics-rare-diseaseTesting.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CodeSystem/CodeSystem-Genomics-rare-diseaseTesting.json b/CodeSystem/CodeSystem-Genomics-rare-diseaseTesting.json index ece4bcc..8bbc7b1 100644 --- a/CodeSystem/CodeSystem-Genomics-rare-diseaseTesting.json +++ b/CodeSystem/CodeSystem-Genomics-rare-diseaseTesting.json @@ -23,7 +23,7 @@ "copyright": "Copyright © 2026+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", "caseSensitive": true, "content": "complete", - "count": 12, + "count": 9, "concept": [ { "code": "sample-storage",