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omarisgreatomarisgreat
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Updates to CodeSystems for Task
Task.businessStatus and Task.statusReason
1 parent 4cd29dd commit a996807

10 files changed

Lines changed: 103 additions & 92 deletions

‎CodeSystem/CodeSystem-Genomics-business-status.json‎

Lines changed: 60 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -8,11 +8,11 @@
88
"value": "business-status-genomics"
99
}
1010
],
11-
"version": "0.2.0",
11+
"version": "0.3.0",
1212
"name": "BusinessStatusGenomics",
1313
"title": "Business Status Genomics",
1414
"status": "draft",
15-
"date": "2022-11-25",
15+
"date": "2024-07-23",
1616
"publisher": "NHS Digital",
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"contact": [
1818
{
@@ -32,32 +32,72 @@
3232
"content": "complete",
3333
"concept": [
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{
35-
"code": "AwaitingSpecimen",
36-
"display": "Awaiting Specimen"
35+
"code": "DeterminingTestRecoverability",
36+
"display": "Determining Test Recoverability"
3737
},
3838
{
39-
"code": "AwaitingRoDAndSpecimen",
40-
"display": "Awaiting Record of Discussion and Specimen"
39+
"code": "TestRecoverable",
40+
"display": "Test Recoverable"
4141
},
4242
{
43-
"code": "SpecimenReceived",
44-
"display": "Specimen Received"
43+
"code": "NotifyingRequesterOfFailure",
44+
"display": "Notifying Requester Of Failure"
4545
},
4646
{
47-
"code": "RemoteProcessingRequired",
48-
"display": "Remote Processing Required"
47+
"code": "SampleRequested",
48+
"display": "Sample Requested (from external lab)"
49+
},
50+
{
51+
"code": "SampleAvailabilityConfirmed",
52+
"display": "Sample Availability Confirmed"
53+
},
54+
{
55+
"code": "SampleBookedIntoLab",
56+
"display": "Sample Booked Into Lab"
57+
},
58+
{
59+
"code": "VariantsPrioritiesListRequired",
60+
"display": "Variants Priorities List Required"
61+
},
62+
{
63+
"code": "VariantsPrioritiesListRetrieved",
64+
"display": "Variants Priorities List Retrieved"
65+
},
66+
{
67+
"code": "PreviousGenomicSequenceDataRequired",
68+
"display": "Previous Genomic Sequence Data Required"
4969
},
5070
{
51-
"code": "AlignSequencing",
52-
"display": "Align Sequencing"
71+
"code": "PreviousGenomicSequenceDataRetrieved",
72+
"display": "Previous Genomic Sequence Data Retrieved"
5373
},
5474
{
55-
"code": "RemoteGeneticDataProcessingRequired",
56-
"display": "Remote Genetic Data Processing Required"
75+
"code": "RemoteSamplePrepRequired",
76+
"display": "Remote Sample Prep Required"
77+
},
78+
{
79+
"code": "SampleSent",
80+
"display": "Sample Sent"
81+
},
82+
{
83+
"code": "SampleReceived",
84+
"display": "Sample Received"
85+
},
86+
{
87+
"code": "SampleStored",
88+
"display": "Sample Stored"
89+
},
90+
{
91+
"code": "FurtherSamplePrepRequired",
92+
"display": "Further Sample Prep Required"
93+
},
94+
{
95+
"code": "RemoteProcessingRequired",
96+
"display": "Remote Processing Required"
5797
},
5898
{
59-
"code": "VariantsIdentified",
60-
"display": "Variants Identified"
99+
"code": "RemoteGenomicDataProcessingRequired",
100+
"display": "Remote Genomic Data Processing Required"
61101
},
62102
{
63103
"code": "RemoteInterpretationRequired",
@@ -72,12 +112,12 @@
72112
"display": "Further Clinical Details Provided"
73113
},
74114
{
75-
"code": "ReflexTestRequired",
76-
"display": "Reflex Test Required"
115+
"code": "ReflexConfirmatoryTestRequired",
116+
"display": "Reflex/Confirmatory Test Required"
77117
},
78118
{
79-
"code": "ReflexTestComplete",
80-
"display": "Reflex Test Complete"
119+
"code": "ReflexConfirmatoryTestComplete",
120+
"display": "Reflex/Confirmatory Test Complete"
81121
}
82122
]
83123
}

‎CodeSystem/CodeSystem-Genomics-task-statusReason.json‎

Lines changed: 24 additions & 44 deletions
Original file line numberDiff line numberDiff line change
@@ -8,11 +8,11 @@
88
"value": "task-statusReason-genomics"
99
}
1010
],
11-
"version": "0.1.0",
11+
"version": "0.2.0",
1212
"name": "TaskStatusReasonGenomics",
1313
"title": "Task StatusReason Genomics",
1414
"status": "draft",
15-
"date": "2023-12-06",
15+
"date": "2024-07-23",
1616
"publisher": "NHS England",
1717
"contact": [
1818
{
@@ -31,73 +31,53 @@
3131
"caseSensitive": true,
3232
"content": "complete",
3333
"concept": [
34-
{
35-
"code": "FurtherClinicalDetailsRequired",
36-
"display": "Further Clinical Details Required"
37-
},
3834
{
39-
"code": "AwaitingSpecimen",
40-
"display": "Awaiting Specimen"
35+
"code": "FurtherInformationNeeded",
36+
"display": "Further Information Needed"
4137
},
4238
{
43-
"code": "AwaitingRoDAndSpecimen",
44-
"display": "Awaiting Record of Discussion and Specimen"
39+
"code": "AwaitingSample",
40+
"display": "Awaiting Sample"
41+
},
42+
{
43+
"code": "AwaitingRoDAndOrSample",
44+
"display": "Awaiting Record of Discussion and/or Sample"
4545
},
4646
{
4747
"code": "InvalidRequest",
4848
"display": "Invalid Request"
4949
},
5050
{
51-
"code": "PipelineActivityFailure",
52-
"display": "Pipeline Activity Failure"
51+
"code": "PipelineError",
52+
"display": "Pipeline Error"
5353
},
5454
{
55-
"code": "TaskTimeExceeded",
56-
"display": "Task Time Exceeded"
55+
"code": "TimeForTaskExceeded",
56+
"display": "Time For Task Exceeded"
5757
},
5858
{
5959
"code": "UnableToInterpret",
6060
"display": "Unable To Interpret"
6161
},
6262
{
63-
"code": "SpecimenReceived",
64-
"display": "SpecimenReceived"
65-
},
66-
{
67-
"code": "SpecimenQualityNotOK",
68-
"display": "Specimen Quality Not OK"
69-
},
70-
{
71-
"code": "TestNoLongerRequired",
72-
"display": "Test No Longer Required"
73-
},
74-
{
75-
"code": "MultipleTestRequestedOnTheSamePatient",
76-
"display": "Multiple Test Requested On The Same Patient(only one test required)"
77-
},
78-
{
79-
"code": "DecisionNotToProgressWithTestRequest",
80-
"display": "Decision Not To Progress With Test Request"
81-
},
82-
{
83-
"code": "TestCouldNotBeDeliveredDueToProcessFailures",
84-
"display": "Test Could Not Be Delivered Due To Process Failures"
63+
"code": "SampleSubOptimal",
64+
"display": "Sample Sub-Optimal"
8565
},
8666
{
87-
"code": "WrongPatient(Mark-in-Error)",
88-
"display": "Wrong Patient (Mark-in-Error)"
67+
"code": "TaskNoLongerRequired",
68+
"display": "Task No Longer Required"
8969
},
9070
{
91-
"code": "SampleAlignedToWrongPatient(Mark-in-Error)",
92-
"display": "Sample Aligned To Wrong Patient (Mark-in-Error)"
71+
"code": "NoSampleProvided",
72+
"display": "No Sample Provided"
9373
},
9474
{
95-
"code": "PatienceChoiceIncorrectlyRecorded(WGS Only)-Mark-in-Error",
96-
"display": "Patience Choice Incorrectly Recorded (WGS Only)-Mark-in-Error"
75+
"code": "ScheduledDelay",
76+
"display": "Scheduled Delay"
9777
},
9878
{
99-
"code": "CorrectionOfClinicalData(Mark-in-Error)",
100-
"display": "Correction Of Clinical Data (Mark-in-Error)"
79+
"code": "AwaitingOrderDetail",
80+
"display": "Awaiting Order Detail"
10181
}
10282
]
10383
}

‎Task/Task-NonWGSRareDiseaseTestOrderAccepted-Example.json‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2,12 +2,12 @@
22
"resourceType": "Task",
33
"id": "Task-NonWGSRareDiseaseTestOrderAccepted-Example",
44
"status": "accepted",
5-
"businessStatus": {
5+
"statusReason": {
66
"coding": [
77
{
88
"system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
9-
"code": "AwaitingSpecimen",
10-
"display": "Awaiting Specimen"
9+
"code": "AwaitingSample",
10+
"display": "Awaiting Sample"
1111
}
1212
]
1313
},

‎Task/Task-NonWGSRareDiseaseTestOrderHold-Example.json‎

Lines changed: 2 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -6,17 +6,8 @@
66
"coding": [
77
{
88
"system": "https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics",
9-
"code": "TaskTimeExceeded",
10-
"display": "Task Time Exceeded"
11-
}
12-
]
13-
},
14-
"businessStatus": {
15-
"coding": [
16-
{
17-
"system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
18-
"code": "AwaitingSpecimen",
19-
"display": "Awaiting Specimen"
9+
"code": "NoSampleProvided",
10+
"display": "NoSampleProvided"
2011
}
2112
]
2213
},

‎Task/Task-WGSRareDiseaseTestOrderAccepted-Example.json‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2,12 +2,12 @@
22
"resourceType": "Task",
33
"id": "Task-WGSRareDiseaseTestOrderAccepted-Example",
44
"status": "on-hold",
5-
"businessStatus": {
5+
"statusReason": {
66
"coding": [
77
{
88
"system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
9-
"code": "AwaitingRoDAndSpecimen",
10-
"display": "Awaiting Record of Discussion and Specimen"
9+
"code": "AwaitingRoDAndOrSample",
10+
"display": "Awaiting Record of Discussion and/or Sample"
1111
}
1212
]
1313
},

‎Task/Task-WGSRareDiseaseTestOrderForwarded-Example.json‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,8 +6,8 @@
66
"coding": [
77
{
88
"system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
9-
"code": "SpecimenReceived",
10-
"display": "Specimen Received"
9+
"code": "SampleReceived",
10+
"display": "Sample Received"
1111
}
1212
]
1313
},

‎Task/UKCore-Task-DPYDSequencingTask-Example-update.json‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -16,12 +16,12 @@
1616
}
1717
],
1818
"status": "accepted",
19-
"businessStatus": {
19+
"statusReason": {
2020
"coding": [
2121
{
2222
"system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
23-
"code": "AwaitingSpecimen",
24-
"display": "Awaiting Specimen"
23+
"code": "AwaitingSample",
24+
"display": "Awaiting Sample"
2525
}
2626
]
2727
},

‎Task/UKCore-Task-DPYDSequencingTask-Example.json‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -19,12 +19,12 @@
1919
}
2020
],
2121
"status": "requested",
22-
"businessStatus": {
22+
"statusReason": {
2323
"coding": [
2424
{
2525
"system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
26-
"code": "AwaitingSpecimen",
27-
"display": "Awaiting Specimen"
26+
"code": "AwaitingSample",
27+
"display": "Awaiting Sample"
2828
}
2929
]
3030
},

‎ValueSet/ValueSet-Genomics-business-status.json‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
1111
"include": [
1212
{
1313
"system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
14-
"version": "0.2.0"
14+
"version": "0.3.0"
1515
}
1616
]
1717
}

‎ValueSet/ValueSet-Genomics-task-statusReason.json‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
"resourceType": "ValueSet",
33
"id": "genomics-task-statusReason",
44
"url": "https://fhir.nhs.uk/ValueSet/task-statusReason-genomics",
5-
"version": "0.1.0",
5+
"version": "0.2.0",
66
"name": "GenomicsTaskStatusReason",
77
"title":"Genomics Task Status Reason",
88
"status": "draft",
@@ -11,7 +11,7 @@
1111
"include": [
1212
{
1313
"system": "https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics",
14-
"version": "0.1.0"
14+
"version": "0.2.0"
1515
}
1616
]
1717
}

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