diff --git a/CodeSystem/CodeSystem-Genomics-AdditionalInfoType.json b/CodeSystem/CodeSystem-Genomics-AdditionalInfoType.json new file mode 100644 index 00000000..8c0186f1 --- /dev/null +++ b/CodeSystem/CodeSystem-Genomics-AdditionalInfoType.json @@ -0,0 +1,58 @@ +{ + "resourceType": "CodeSystem", + "id": "AdditionalInfoTypeGenomics", + "url": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "version": "0.1.0", + "name": "AdditionalInfoTypeGenomics", + "title": "Additional Information Type Genomics", + "status": "draft", + "date": "2024-05-31T00:00:00.000Z", + "publisher": "NHS England", + "contact": [ + { + "name": "NHS England", + "telecom": [ + { + "system": "email", + "value": "interoperabilityteam@nhs.net" + } + ] + } + ], + "description": "CodeSystem to specify reference to additional details of the input's use as part of the task execution or the output generated from task completion.", + "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": [ + { + "code": "Consent", + "display": "Consent", + "definition": "Consent for treatment record" + }, + { + "code": "ConsignmentNumber", + "display": "Consignment Number", + "definition": "The specimen consignment number" + }, + { + "code": "DiagnosticReport", + "display": "DiagnosticReport", + "definition": "The DiagnosticReport generated upon the task completion" + }, + { + "code": "RackId", + "display": "Rack Number", + "definition": "The specimen rack number" + }, + { + "code": "Specimen", + "display": "Specimen", + "definition": "The specimen provided for the task execution" + }, + { + "code": "WellId", + "display": "Well Identification Number", + "definition": "The specimen well identification number" + } + ] +} \ No newline at end of file diff --git a/Specimen/Specimen-BloodEDTA-WithCollectoinDetails-Example.json b/Specimen/Specimen-BloodEDTA-WithCollectoinDetails-Example.json index 9737207f..8c984d04 100644 --- a/Specimen/Specimen-BloodEDTA-WithCollectoinDetails-Example.json +++ b/Specimen/Specimen-BloodEDTA-WithCollectoinDetails-Example.json @@ -3,7 +3,7 @@ "id": "Specimen-BloodEDTA-WithCollectoinDetails-Example", "identifier": [ { - "system": "https://fhir.leedsth.nhs.uk//Id/specimenId", + "system": "https://fhir.leedsth.nhs.uk/Id/specimenId", "value": "RR8-696B0-17843" } ], diff --git a/StructureDefinition/NHSDigital-Task-Genomics.StructureDefinition.json b/StructureDefinition/NHSDigital-Task-Genomics.StructureDefinition.json index c4812b85..6b0df191 100644 --- a/StructureDefinition/NHSDigital-Task-Genomics.StructureDefinition.json +++ b/StructureDefinition/NHSDigital-Task-Genomics.StructureDefinition.json @@ -154,6 +154,22 @@ ] } ] + }, + { + "id": "Task.input.type.coding", + "path": "Task.input.type.coding", + "binding": { + "strength": "preferred", + "valueSet": "https://fhir.nhs.uk/ValueSet/AdditionalInfoTypeGenomics" + } + }, + { + "id": "Task.output.type.coding", + "path": "Task.output.type.coding", + "binding": { + "strength": "preferred", + "valueSet": "https://fhir.nhs.uk/ValueSet/AdditionalInfoTypeGenomics" + } } ] } diff --git a/Task/Task-NonWGSRareDiseaseTestOrderAccepted-SufficientSample-Example.json b/Task/Task-NonWGSRareDiseaseTestOrderAccepted-SufficientSample-Example.json index b50229ce..b58f6a98 100644 --- a/Task/Task-NonWGSRareDiseaseTestOrderAccepted-SufficientSample-Example.json +++ b/Task/Task-NonWGSRareDiseaseTestOrderAccepted-SufficientSample-Example.json @@ -49,13 +49,30 @@ "text": "Optional Free Text field to record any additional details" } ], + "input": [ + { + "type": { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "ConsignmentNumber", + "display": "Consignment Number" + } + ] + }, + "valueIdentifier": { + "system": "https://www.royalmail.com/track-your-item#/", + "value": "HZ970705811GB" + } + } + ], "output": [ { "type": { - "coding": [ + "coding": [ { - "system": "http://snomed.info/sct", - "code": "123038009", + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "Specimen", "display": "Specimen" } ] diff --git a/Task/Task-NonWGSRareDiseaseTestOrderCompleted-CascadeTestingExample.json b/Task/Task-NonWGSRareDiseaseTestOrderCompleted-CascadeTestingExample.json index 9a78aeae..7898dede 100644 --- a/Task/Task-NonWGSRareDiseaseTestOrderCompleted-CascadeTestingExample.json +++ b/Task/Task-NonWGSRareDiseaseTestOrderCompleted-CascadeTestingExample.json @@ -45,9 +45,9 @@ "type": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "1054161000000101", - "display": "Genetic report (record artifact)" + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "DiagnosticReport", + "display": "DiagnosticReport" } ] }, diff --git a/Task/Task-NonWGSRareDiseaseTestOrderCompleted-FollowupTest-Example.json b/Task/Task-NonWGSRareDiseaseTestOrderCompleted-FollowupTest-Example.json index 63f58d4f..75fcd30c 100644 --- a/Task/Task-NonWGSRareDiseaseTestOrderCompleted-FollowupTest-Example.json +++ b/Task/Task-NonWGSRareDiseaseTestOrderCompleted-FollowupTest-Example.json @@ -45,9 +45,9 @@ "type": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "1054161000000101", - "display": "Genetic report (record artifact)" + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "DiagnosticReport", + "display": "DiagnosticReport" } ] }, diff --git a/Task/Task-NonWGSRareDiseaseTestOrderForwareded-CancerSolidTumor-Example.json b/Task/Task-NonWGSRareDiseaseTestOrderForwareded-CancerSolidTumor-Example.json index e60003bd..306967ac 100644 --- a/Task/Task-NonWGSRareDiseaseTestOrderForwareded-CancerSolidTumor-Example.json +++ b/Task/Task-NonWGSRareDiseaseTestOrderForwareded-CancerSolidTumor-Example.json @@ -40,13 +40,13 @@ "text": "Free to capture additional comments" } ], - "input": [ + "input": [ { "type": { - "coding": [ + "coding": [ { - "system": "http://snomed.info/sct", - "code": "123038009", + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "Specimen", "display": "Specimen" } ] diff --git a/Task/Task-NonWGSRareDiseaseTestOrderRejected-InsufficientSample-Example.json b/Task/Task-NonWGSRareDiseaseTestOrderRejected-InsufficientSample-Example.json index 58f0e4b0..755099c4 100644 --- a/Task/Task-NonWGSRareDiseaseTestOrderRejected-InsufficientSample-Example.json +++ b/Task/Task-NonWGSRareDiseaseTestOrderRejected-InsufficientSample-Example.json @@ -49,13 +49,36 @@ "text": "Please provide additional sample of X" } ], - "output": [ + "input": [ { "type": { - "coding": [ + "coding": [ { - "system": "http://snomed.info/sct", - "code": "123038009", + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "RackId", + "display": "Rack Number" + } + ] + }, + "valueIdentifier": { + "system": "https://www.guysandstthomas.nhs.uk/RackId", + "value": "RJ1-RAX01-9449307555", + "assigner": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "RJ1" + } + } + } + } + ], + "output": [ + { + "type": { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "Specimen", "display": "Specimen" } ] diff --git a/Task/Task-NonWGSTestOrderFormAccepted-UsingStoredSample-Example.json b/Task/Task-NonWGSTestOrderFormAccepted-UsingStoredSample-Example.json index 888dd40b..d74eb9c7 100644 --- a/Task/Task-NonWGSTestOrderFormAccepted-UsingStoredSample-Example.json +++ b/Task/Task-NonWGSTestOrderFormAccepted-UsingStoredSample-Example.json @@ -39,14 +39,37 @@ "text": "Test critieria met and sample to be used from storage" } ], + "input": [ + { + "type": { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "WellId", + "display": "Well Identification Number" + } + ] + }, + "valueIdentifier": { + "system": "https://www.guysandstthomas.nhs.uk/WellId", + "value": "RJ1-WID-9449307555", + "assigner": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "RJ1" + } + } + } + } + ], "output": [ { "type": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "445295009", - "display": "Blood specimen with EDTA" + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "Specimen", + "display": "Specimen" } ] }, diff --git a/Task/Task-TestOrderFormAccepted-StorageOfMaterial-Example.json b/Task/Task-TestOrderFormAccepted-StorageOfMaterial-Example.json index 1ebb90d8..74bd850c 100644 --- a/Task/Task-TestOrderFormAccepted-StorageOfMaterial-Example.json +++ b/Task/Task-TestOrderFormAccepted-StorageOfMaterial-Example.json @@ -45,9 +45,9 @@ "type": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "445295009", - "display": "Blood specimen with EDTA" + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "Specimen", + "display": "Specimen" } ] }, diff --git a/Task/Task-WGSRareDiseaseTestOrderAccepted-DirectToLab-Example.json b/Task/Task-WGSRareDiseaseTestOrderAccepted-DirectToLab-Example.json index a4df2644..88191089 100644 --- a/Task/Task-WGSRareDiseaseTestOrderAccepted-DirectToLab-Example.json +++ b/Task/Task-WGSRareDiseaseTestOrderAccepted-DirectToLab-Example.json @@ -2,22 +2,22 @@ "resourceType": "Task", "id": "Task-WGSRareDiseaseTestOrderAccepted-DirectToLab-Example", "status": "accepted", - "statusReason": { + "statusReason": { "coding": [ - { - "system": "https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics", - "code": "SpecimenReceived", + { + "system": "https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics", + "code": "SpecimenReceived", "display": "Specimen Received" } ] }, "intent": "order", "priority": "urgent", - "code": { + "code": { "coding": [ - { - "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics", - "code": "RequestSampleAlignment", + { + "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics", + "code": "RequestSampleAlignment", "display": "Request & Sample Alignment" } ] @@ -33,7 +33,7 @@ } }, "authoredOn": "2023-10-01T15:00:00Z", - "lastModified":"2023-10-10T16:00:00Z", + "lastModified": "2023-10-10T16:00:00Z", "requester": { "reference": "PractitionerRole/PractitionerRole-EugeneSmith-Example" }, @@ -47,10 +47,10 @@ "output": [ { "type": { - "coding": [ + "coding": [ { - "system": "http://snomed.info/sct", - "code": "123038009", + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "Specimen", "display": "Specimen" } ] @@ -60,4 +60,4 @@ } } ] -} +} \ No newline at end of file diff --git a/Task/Task-WGSRareDiseaseTestOrderAccepted-TrioTestingProband-Example.json b/Task/Task-WGSRareDiseaseTestOrderAccepted-TrioTestingProband-Example.json index c4ef936d..6a55eec1 100644 --- a/Task/Task-WGSRareDiseaseTestOrderAccepted-TrioTestingProband-Example.json +++ b/Task/Task-WGSRareDiseaseTestOrderAccepted-TrioTestingProband-Example.json @@ -54,9 +54,9 @@ "type": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "445295009", - "display": "Blood specimen with EDTA" + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "Specimen", + "display": "Specimen" } ] }, @@ -68,9 +68,9 @@ "type": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "445295009", - "display": "Blood specimen with EDTA" + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "Specimen", + "display": "Specimen" } ] }, @@ -82,9 +82,9 @@ "type": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "445295009", - "display": "Blood specimen with EDTA" + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "Specimen", + "display": "Specimen" } ] }, @@ -96,9 +96,9 @@ "type": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "886971000000109", - "display": "Consent for treatment record" + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "Consent", + "display": "Consent" } ] }, @@ -110,9 +110,9 @@ "type": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "886971000000109", - "display": "Consent for treatment record" + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "Consent", + "display": "Consent" } ] }, @@ -124,9 +124,9 @@ "type": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "886971000000109", - "display": "Consent for treatment record" + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "Consent", + "display": "Consent" } ] }, diff --git a/Task/Task-WGSRareDiseaseTestOrderCompleted-DirectToLab-Example.json b/Task/Task-WGSRareDiseaseTestOrderCompleted-DirectToLab-Example.json index c098de12..fc1f1b98 100644 --- a/Task/Task-WGSRareDiseaseTestOrderCompleted-DirectToLab-Example.json +++ b/Task/Task-WGSRareDiseaseTestOrderCompleted-DirectToLab-Example.json @@ -45,9 +45,9 @@ "type": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "1054161000000101", - "display": "Genetic report (record artifact)" + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "DiagnosticReport", + "display": "DiagnosticReport" } ] }, diff --git a/Task/Task-WGSRareDiseaseTestOrderCompleted-TrioTestingProband-Example.json b/Task/Task-WGSRareDiseaseTestOrderCompleted-TrioTestingProband-Example.json index 21d08c49..1b3ccb0a 100644 --- a/Task/Task-WGSRareDiseaseTestOrderCompleted-TrioTestingProband-Example.json +++ b/Task/Task-WGSRareDiseaseTestOrderCompleted-TrioTestingProband-Example.json @@ -45,9 +45,9 @@ "type": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "1054161000000101", - "display": "Genetic report (record artifact)" + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "DiagnosticReport", + "display": "DiagnosticReport" } ] }, diff --git a/Task/Task-WGSRareDiseaseTestOrderForwarded-Example.json b/Task/Task-WGSRareDiseaseTestOrderForwarded-Example.json index d5758dae..2670fb54 100644 --- a/Task/Task-WGSRareDiseaseTestOrderForwarded-Example.json +++ b/Task/Task-WGSRareDiseaseTestOrderForwarded-Example.json @@ -49,8 +49,8 @@ "type": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "123038009", + "system": "https://fhir.nhs.uk/CodeSystem/AdditionalInfoTypeGenomics", + "code": "Specimen", "display": "Specimen" } ] diff --git a/ValueSet/ValueSet-Genomics-AdditionalInfoType.json b/ValueSet/ValueSet-Genomics-AdditionalInfoType.json new file mode 100644 index 00000000..c8c75f5c --- /dev/null +++ b/ValueSet/ValueSet-Genomics-AdditionalInfoType.json @@ -0,0 +1,30 @@ +{ + "resourceType": "ValueSet", + "url": "https://fhir.nhs.uk/ValueSet/AdditionalInfoTypeGenomics", + "version": "0.1.0", + "name": "AdditionalInfoTypeGenomics", + "title": "Additional Information Type Genomics", + "status": "draft", + "date": "2024-05-31T00:00:00.000Z", + "publisher": "NHS England", + "contact": [ + { + "name": "NHS England", + "telecom": [ + { + "system": "email", + "value": "interoperabilityteam@nhs.net" + } + ] + } + ], "description": "ValueSet to specify reference to additional details of the input`s use as part of the task execution or the output generated from task completion.", + "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/AdditionalInfoTypeGenomics", + "version": "0.1.0" + } + ] + } +} \ No newline at end of file