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Merged
KazeemHamzat merged 5 commits into from
Jun 5, 2024
Merged

Create CodeSystems AdditionalInfoTypeGenomics #74

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559b087
Create CodeSystems AdditionalInfoTypeGenomics
KazeemHamzat May 31, 2024
42faea6
Update to Examples using CodeSystem-Genomics-AdditionalInfoType
KazeemHamzat Jun 3, 2024
399c094
Update ask-WGSRareDiseaseTestOrderAccepted-TrioTestingProband-Example
KazeemHamzat Jun 3, 2024
7588811
Create to consignment Num, RackId & WellId in Examples
KazeemHamzat Jun 3, 2024
7129cbc
Remove White Space ask-NonWGSRareDiseaseTestOrderForwareded-CancerSol…
KazeemHamzat Jun 5, 2024
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58 changes: 58 additions & 0 deletions CodeSystem/CodeSystem-Genomics-AdditionalInfoType.json
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{
"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"
}
]
}
2 changes: 1 addition & 1 deletion Specimen/Specimen-BloodEDTA-WithCollectoinDetails-Example.json
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"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"
}
],
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16 changes: 16 additions & 0 deletions StructureDefinition/NHSDigital-Task-Genomics.StructureDefinition.json
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Expand Up @@ -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"
}
}
]
}
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23 changes: 20 additions & 3 deletions Task/Task-NonWGSRareDiseaseTestOrderAccepted-SufficientSample-Example.json
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"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"
}
]
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6 changes: 3 additions & 3 deletions Task/Task-NonWGSRareDiseaseTestOrderCompleted-CascadeTestingExample.json
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Expand Up @@ -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"
}
]
},
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6 changes: 3 additions & 3 deletions Task/Task-NonWGSRareDiseaseTestOrderCompleted-FollowupTest-Example.json
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"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"
}
]
},
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8 changes: 4 additions & 4 deletions Task/Task-NonWGSRareDiseaseTestOrderForwareded-CancerSolidTumor-Example.json
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Expand Up @@ -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"
}
]
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31 changes: 27 additions & 4 deletions Task/Task-NonWGSRareDiseaseTestOrderRejected-InsufficientSample-Example.json
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Expand Up @@ -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"
}
]
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29 changes: 26 additions & 3 deletions Task/Task-NonWGSTestOrderFormAccepted-UsingStoredSample-Example.json
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"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"
}
]
},
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6 changes: 3 additions & 3 deletions Task/Task-TestOrderFormAccepted-StorageOfMaterial-Example.json
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Expand Up @@ -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"
}
]
},
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26 changes: 13 additions & 13 deletions Task/Task-WGSRareDiseaseTestOrderAccepted-DirectToLab-Example.json
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Expand Up @@ -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"
}
]
Expand All @@ -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"
},
Expand All @@ -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"
}
]
Expand All @@ -60,4 +60,4 @@
}
}
]
}
}
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