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Fix patient gender coding #100

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merged 12 commits into from
Feb 4, 2025
Merged

Fix patient gender coding #100

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748297e
Revert "patch: deactivate the workflow"
ir4y Jan 30, 2025
9582910
Fix terminology discrepancy
ir4y Jan 30, 2025
a1e9add
Don't fail the pipeline in case of validaiton error
ir4y Jan 30, 2025
6678b24
Restore text for medications
ir4y Feb 3, 2025
7098006
Restore lowercase text for MedicationRequest
ir4y Feb 3, 2025
9061e23
Update generated files
ir4y Feb 3, 2025
6c12cac
Transcribed coding display corrections into source spreadsheet and ex…
heathfrankel Feb 3, 2025
685f7ea
Update generated files
heathfrankel Feb 3, 2025
c31ff51
Added genderIdentity system and recordedSexOrGender type and value sy…
heathfrankel Feb 3, 2025
0e4fc86
Update generated files
heathfrankel Feb 3, 2025
e8e9e08
Corrected Patient recordedSexOrGender type display
heathfrankel Feb 3, 2025
ccf16e7
Update generated files
heathfrankel Feb 3, 2025
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8 changes: 4 additions & 4 deletions .github/report/action.yml
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Expand Up @@ -98,7 +98,7 @@ runs:
repo: context.repo.repo,
body: comment
})
- shell: bash
name: Fail in case of validation errors
if: steps.has-validation-errors.outputs.errors != '0'
run: exit -1
# - shell: bash
# name: Fail in case of validation errors
# if: steps.has-validation-errors.outputs.errors != '0'
# run: exit -1
0 ...validate.yaml.deactivated.as.it.is.broken → .github/workflows/validate.yaml
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15 changes: 12 additions & 3 deletions Sparked.Csv2FhirMapping/Maps/CSV2Patient.map
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Expand Up @@ -383,7 +383,10 @@ group ToPatient(source src : PatientCSV, target tgt : Patient) {
t_extension.extension as t_ext_value first then {
s_individual_genderIdentity -> t_ext_value.url = 'value',
t_ext_value.value = create('CodeableConcept') as t_value then {
s_individual_genderIdentity -> t_value.coding = c('http://snomed.info/sct', s_individual_genderIdentity) as t_coding then {
src.individual_genderIdentity_value_system where length() = 0 -> t_value.coding = c('http://snomed.info/sct', s_individual_genderIdentity) as t_coding then {
src.individual_genderIdentity_value_display as s_display where length() > 0 -> t_coding.display = s_display;
};
src.individual_genderIdentity_value_system as s_system where length() > 0 -> t_value.coding = c(s_system, s_individual_genderIdentity) as t_coding then {
src.individual_genderIdentity_value_display as s_display where length() > 0 -> t_coding.display = s_display;
};
};
Expand Down Expand Up @@ -431,7 +434,10 @@ group ToPatient(source src : PatientCSV, target tgt : Patient) {
t_extension.extension as t_ext_type first then {
s_recordedSexOrGender_type -> t_ext_type.url = 'type',
t_ext_type.value = create('CodeableConcept') as t_value then {
s_recordedSexOrGender_type -> t_value.coding = c('http://snomed.info/sct', s_recordedSexOrGender_type) as t_coding then {
src.individual_recordedSexOrGender_type_system where length() = 0 -> t_value.coding = c('http://snomed.info/sct', s_recordedSexOrGender_type) as t_coding then {
src.individual_recordedSexOrGender_type_text as s_display where length() > 0 -> t_coding.display = s_display;
};
src.individual_recordedSexOrGender_type_system as s_system where length() > 0 -> t_value.coding = c(s_system, s_recordedSexOrGender_type) as t_coding then {
src.individual_recordedSexOrGender_type_text as s_display where length() > 0 -> t_coding.display = s_display;
};
};
Expand All @@ -440,7 +446,10 @@ group ToPatient(source src : PatientCSV, target tgt : Patient) {
src.individual_recordedSexOrGender_value_code as s_recordedSexOrGender_value where length() > 0 -> t_extension.extension as t_ext_value first then {
s_recordedSexOrGender_value -> t_ext_value.url = 'value',
t_ext_value.value = create('CodeableConcept') as t_value then {
s_recordedSexOrGender_value -> t_value.coding = c('http://snomed.info/sct', s_recordedSexOrGender_value) as t_coding then {
src.individual_recordedSexOrGender_value_system where length() = 0 -> t_value.coding = c('http://snomed.info/sct', s_recordedSexOrGender_value) as t_coding then {
src.individual_recordedSexOrGender_value_text as s_display where length() > 0 -> t_coding.display = s_display;
};
src.individual_recordedSexOrGender_value_system as s_system where length() > 0 -> t_value.coding = c(s_system, s_recordedSexOrGender_value) as t_coding then {
src.individual_recordedSexOrGender_value_text as s_display where length() > 0 -> t_coding.display = s_display;
};
};
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2 changes: 1 addition & 1 deletion generated/Immunization-zoster-missing-occurrence.json
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Expand Up @@ -21,7 +21,7 @@
{
"system": "http://snomed.info/sct",
"code": "830851000168105",
"display": "varicella-zoster live vaccine"
"display": "Varicella-zoster live vaccine"
}
]
},
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2 changes: 1 addition & 1 deletion generated/Immunization-zoster-notgiven.json
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Expand Up @@ -21,7 +21,7 @@
{
"system": "http://snomed.info/sct",
"code": "830851000168105",
"display": "varicella-zoster live vaccine"
"display": "Varicella-zoster live vaccine"
}
]
},
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2 changes: 1 addition & 1 deletion generated/Immunization-zoster-suppressed-subject.json
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Expand Up @@ -21,7 +21,7 @@
{
"system": "http://snomed.info/sct",
"code": "830851000168105",
"display": "varicella-zoster live vaccine"
"display": "Varicella-zoster live vaccine"
}
]
},
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2 changes: 1 addition & 1 deletion generated/Medication-metformin-mpp.json
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Expand Up @@ -11,7 +11,7 @@
{
"system": "http://snomed.info/sct",
"code": "28037011000036102",
"display": "metformin hydrochloride 500 mg tablet, 100"
"display": "Metformin hydrochloride 500 mg tablet, 100"
}
]
},
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2 changes: 1 addition & 1 deletion generated/Medication-perindopril-amlodipine-mpp.json
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Expand Up @@ -11,7 +11,7 @@
{
"system": "http://snomed.info/sct",
"code": "86430011000036105",
"display": "perindopril arginine 10 mg + amlodipine 10 mg tablet, 30"
"display": "Perindopril arginine 10 mg + amlodipine 10 mg tablet, 30"
}
]
},
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2 changes: 1 addition & 1 deletion generated/MedicationRequest-atorvastatin-instance.json
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Expand Up @@ -13,7 +13,7 @@
{
"system": "http://snomed.info/sct",
"code": "22784011000036109",
"display": "atorvastatin 20 mg tablet"
"display": "Atorvastatin 20 mg tablet"
}
]
},
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2 changes: 1 addition & 1 deletion generated/MedicationRequest-atorvastatin.json
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Expand Up @@ -13,7 +13,7 @@
{
"system": "http://snomed.info/sct",
"code": "27437011000036101",
"display": "atorvastatin 20 mg tablet, 30"
"display": "Atorvastatin 20 mg tablet, 30"
}
]
},
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2 changes: 1 addition & 1 deletion generated/MedicationRequest-klacid.json
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Expand Up @@ -20,7 +20,7 @@
{
"system": "http://snomed.info/sct",
"code": "27908011000036108",
"display": "clarithromycin 250 mg tablet, 100"
"display": "Clarithromycin 250 mg tablet, 100"
}
],
"text": "clarithromycin 250 mg tablet, 100"
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2 changes: 1 addition & 1 deletion generated/MedicationRequest-metformin-contained.json
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Expand Up @@ -20,7 +20,7 @@
{
"system": "http://snomed.info/sct",
"code": "28037011000036102",
"display": "metformin hydrochloride 500 mg tablet, 100"
"display": "Metformin hydrochloride 500 mg tablet, 100"
}
],
"text": "metformin hydrochloride 500 mg tablet, 100"
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2 changes: 1 addition & 1 deletion generated/MedicationRequest-paracetamol-codeine.json
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Expand Up @@ -13,7 +13,7 @@
{
"system": "http://snomed.info/sct",
"code": "79115011000036100",
"display": "paracetamol 500 mg + codeine phosphate hemihydrate 30 mg tablet"
"display": "Paracetamol 500 mg + codeine phosphate hemihydrate 30 mg tablet"
}
]
},
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2 changes: 1 addition & 1 deletion generated/MedicationRequest-simvastatin-pbs.json
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Expand Up @@ -18,7 +18,7 @@
{
"system": "http://snomed.info/sct",
"code": "28213011000036109",
"display": "simvastatin 40 mg tablet, 30"
"display": "Simvastatin 40 mg tablet, 30"
}
],
"text": "simvastatin 40 mg tablet, 30 tablets"
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2 changes: 1 addition & 1 deletion generated/Observation-waistcircum-1-position.json
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Expand Up @@ -65,7 +65,7 @@
{
"system": "http://snomed.info/sct",
"code": "10904000",
"display": "Orthostatic body position"
"display": "Orthostatic body position"
}
],
"text": "Standing"
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2 changes: 1 addition & 1 deletion generated/Organization-alice-springs-medical-practice.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8511",
"display": "General Practice"
"display": "General Practice Medical Services"
},
{
"system": "http://snomed.info/sct",
Expand Down
2 changes: 1 addition & 1 deletion generated/Organization-annie-river-practice.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8511",
"display": "General Practice"
"display": "General Practice Medical Services"
},
{
"system": "http://snomed.info/sct",
Expand Down
2 changes: 1 addition & 1 deletion generated/Organization-appin-pharmacy.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "4271",
"display": "Retail Pharmacy"
"display": "Pharmaceutical, Cosmetic and Toiletry Goods Retailing"
},
{
"system": "http://snomed.info/sct",
Expand Down
2 changes: 1 addition & 1 deletion generated/Organization-balbarrup-practice.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8511",
"display": "General Practice"
"display": "General Practice Medical Services"
},
{
"system": "http://snomed.info/sct",
Expand Down
2 changes: 1 addition & 1 deletion generated/Organization-barney-view-private-hospital.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8401",
"display": "Hospitals (except Psychiatric Hospitals)"
"display": "Hospitals (Except Psychiatric Hospitals)"
},
{
"system": "http://snomed.info/sct",
Expand Down
2 changes: 1 addition & 1 deletion generated/Organization-beltana-medical-practice.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8511",
"display": "General Practice"
"display": "General Practice Medical Services"
},
{
"system": "http://snomed.info/sct",
Expand Down
2 changes: 1 addition & 1 deletion generated/Organization-beswick-private-hospital.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8401",
"display": "Hospitals (except Psychiatric Hospitals)"
"display": "Hospitals (Except Psychiatric Hospitals)"
},
{
"system": "http://snomed.info/sct",
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2 changes: 1 addition & 1 deletion generated/Organization-bunbury-public-hospital.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8401",
"display": "Hospitals (except Psychiatric Hospitals)"
"display": "Hospitals (Except Psychiatric Hospitals)"
},
{
"system": "http://snomed.info/sct",
Expand Down
2 changes: 1 addition & 1 deletion generated/Organization-bungabbee-medical-clinic.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8511",
"display": "General Practice"
"display": "General Practice Medical Services"
},
{
"system": "http://snomed.info/sct",
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2 changes: 1 addition & 1 deletion generated/Organization-cracow-pharmacy.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "4271",
"display": "Retail Pharmacy"
"display": "Pharmaceutical, Cosmetic and Toiletry Goods Retailing"
},
{
"system": "http://snomed.info/sct",
Expand Down
2 changes: 1 addition & 1 deletion generated/Organization-cullen-bay-medical-clinic.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8511",
"display": "General Practice"
"display": "General Practice Medical Services"
},
{
"system": "http://snomed.info/sct",
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2 changes: 1 addition & 1 deletion generated/Organization-east-mackay-pharmacy.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "4271",
"display": "Retail Pharmacy"
"display": "Pharmaceutical, Cosmetic and Toiletry Goods Retailing"
},
{
"system": "http://snomed.info/sct",
Expand Down
2 changes: 1 addition & 1 deletion generated/Organization-edwardstown-pharmacy.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "4271",
"display": "Retail Pharmacy"
"display": "Pharmaceutical, Cosmetic and Toiletry Goods Retailing"
},
{
"system": "http://snomed.info/sct",
Expand Down
2 changes: 1 addition & 1 deletion generated/Organization-elimbah-medical-centre.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8511",
"display": "General Practice"
"display": "General Practice Medical Services"
},
{
"system": "http://snomed.info/sct",
Expand Down
2 changes: 1 addition & 1 deletion generated/Organization-ginninderra-pharmacy.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "4271",
"display": "Retail Pharmacy"
"display": "Pharmaceutical, Cosmetic and Toiletry Goods Retailing"
},
{
"system": "http://snomed.info/sct",
Expand Down
2 changes: 1 addition & 1 deletion generated/Organization-glennie-heights-public-hospital.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8401",
"display": "Hospitals (except Psychiatric Hospitals)"
"display": "Hospitals (Except Psychiatric Hospitals)"
},
{
"system": "http://snomed.info/sct",
Expand Down
2 changes: 1 addition & 1 deletion generated/Organization-joyces-creek-medical-clinic.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8511",
"display": "General Practice"
"display": "General Practice Medical Services"
},
{
"system": "http://snomed.info/sct",
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2 changes: 1 addition & 1 deletion generated/Organization-kensington-public-hospital.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8401",
"display": "Hospitals (except Psychiatric Hospitals)"
"display": "Hospitals (Except Psychiatric Hospitals)"
},
{
"system": "http://snomed.info/sct",
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2 changes: 1 addition & 1 deletion generated/Organization-lake-wells-medical-practice.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8511",
"display": "General Practice"
"display": "General Practice Medical Services"
},
{
"system": "http://snomed.info/sct",
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2 changes: 1 addition & 1 deletion generated/Organization-launceston-pharmacy.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "4271",
"display": "Retail Pharmacy"
"display": "Pharmaceutical, Cosmetic and Toiletry Goods Retailing"
},
{
"system": "http://snomed.info/sct",
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2 changes: 1 addition & 1 deletion generated/Organization-launching-place-pharmacy.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "4271",
"display": "Retail Pharmacy"
"display": "Pharmaceutical, Cosmetic and Toiletry Goods Retailing"
},
{
"system": "http://snomed.info/sct",
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2 changes: 1 addition & 1 deletion generated/Organization-leasingham-public-hospital.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8401",
"display": "Hospitals (except Psychiatric Hospitals)"
"display": "Hospitals (Except Psychiatric Hospitals)"
},
{
"system": "http://snomed.info/sct",
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2 changes: 1 addition & 1 deletion generated/Organization-lilydale-pharmacy.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "4271",
"display": "Retail Pharmacy"
"display": "Pharmaceutical, Cosmetic and Toiletry Goods Retailing"
},
{
"system": "http://snomed.info/sct",
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2 changes: 1 addition & 1 deletion generated/Organization-loch-lomond-medical-clinic.json
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Expand Up @@ -40,7 +40,7 @@
{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8511",
"display": "General Practice"
"display": "General Practice Medical Services"
},
{
"system": "http://snomed.info/sct",
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2 changes: 1 addition & 1 deletion generated/Organization-ludmilla-pharmacy.json
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{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "4271",
"display": "Retail Pharmacy"
"display": "Pharmaceutical, Cosmetic and Toiletry Goods Retailing"
},
{
"system": "http://snomed.info/sct",
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2 changes: 1 addition & 1 deletion generated/Organization-mcbeath-pharmacy.json
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{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "4271",
"display": "Retail Pharmacy"
"display": "Pharmaceutical, Cosmetic and Toiletry Goods Retailing"
},
{
"system": "http://snomed.info/sct",
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2 changes: 1 addition & 1 deletion generated/Organization-milnes-bridge-medical-centre.json
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{
"system": "http://www.abs.gov.au/ausstats/[email protected]/mf/1292.0",
"code": "8511",
"display": "General Practice"
"display": "General Practice Medical Services"
},
{
"system": "http://snomed.info/sct",
Expand Down
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