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Examples of proposed FHIR structure for Global.HealthxISARIC #205

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Examples of proposed FHIR structure for Global.HealthxISARIC #205

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94e0852
first draft Patient structure
pipliggins Dec 7, 2023
09277c6
update gitignore
pipliggins Dec 7, 2023
94b5ebb
first draft example condition, meds
pipliggins Dec 13, 2023
b72a163
observation examples
pipliggins Dec 13, 2023
80e49b7
Add outcome observation example
pipliggins Jan 3, 2024
b472a37
Add possible timing extension for observations
pipliggins Jan 5, 2024
cde29a9
Add Encounter example
pipliggins Jan 8, 2024
8a68eb1
Add location to encounter
pipliggins Jan 8, 2024
b471b06
Add procedure example
pipliggins Jan 8, 2024
0cd9e4d
Add draft ResearchSubject
pipliggins Jan 8, 2024
bdfbf4e
1st draft ResearchStudy resource
pipliggins Jan 10, 2024
8c3d8c8
Previous export file for isaric schema -> fhir
pipliggins Jan 10, 2024
2366bf7
Edits to observation, rStudy, encounter
pipliggins Jan 17, 2024
fc38034
Add organization
pipliggins Jan 24, 2024
8e7fb00
Fix indentation
pipliggins Jan 24, 2024
074adaa
Initial draft for converting FHIR resources to FHIRflat files
pipliggins Jan 29, 2024
e5a3ade
Create specimen.json
pipliggins Feb 2, 2024
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4 changes: 4 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -143,6 +143,7 @@ venv/
ENV/
env.bak/
venv.bak/
isaric-venv

# Spyder project settings
.spyderproject
Expand All @@ -151,6 +152,9 @@ venv.bak/
# Rope project settings
.ropeproject

# VScode project settings
.vscode

# mkdocs documentation
/site

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284 changes: 284 additions & 0 deletions fhir/resource_structure_dev/condition.json
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{
"resourceType": "Condition",
"id": "example-symptom-present",
"meta" : {
"profile" : [
"our_url_here"
]
},
"category": [
{
"coding": [
{
"code": "75325-1",
"system": "http://loinc.org",
"display": "Symptom"
}
]
}
],
"code": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "49727002",
"display": "Cough"
}
]
},
"verificationStatus": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status",
"code": "confirmed",
"display": "Confirmed"
},
{
"system": "http://snomed.info/sct",
"code": "410605003",
"display": "Confirmed present (qualifier value)"
}
]
},
"clinicalStatus": {
"coding": [
{
"code": "active",
"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
"display": "Active"
}
]
},
"severity": {
"coding": [
{
"code": "24484000",
"system": "http://snomed.info/sct",
"display": "Severe"
}
]
},
"subject": {
"reference": "Patient/<id>"
},
"recordedDate": "2020-10-05"
},

{
"resourceType": "Condition",
"id": "example-symptom-absent",
"meta" : {
"profile" : [
"our_url_here"
]
},
"category": [
{
"coding": [
{
"code": "75325-1",
"system": "http://loinc.org",
"display": "Symptom"
}
]
}
],
"code": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "40917007",
"display": "Clouded consciousness"
}
]
},
"verificationStatus": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status",
"code": "refuted",
"display": "Refuted"
},
{
"system": "http://snomed.info/sct",
"code": "410594000",
"display": "Definitely NOT present (qualifier value)"
}
]
},
"subject": {
"reference": "Patient/<id>"
},
"recordedDate": "2020-10-05"
}

{
"resourceType": "Condition",
"id": "chronic-condition-present",
"meta" : {
"profile" : [
"our_url_here"
]
},
"category": [
{
"coding": [
{
"code": "392521001",
"system": "http://snomed.info/sct",
"display": "History of (contextual qualifier) (qualifier value)"
}
]
}
],
"verificationStatus": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status",
"code": "confirmed",
"display": "Confirmed"
},
{
"system": "http://snomed.info/sct",
"code": "410605003",
"display": "Confirmed present (qualifier value)"
}
]
},
"clinicalStatus": {
"coding": [
{
"code": "active",
"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
"display": "Active"
}
]
},
"code": {
"coding": [
{
"code": "709044004",
"system": "http://snomed.info/sct",
"display": "Chronic kidney disease (disorder)"
}
]
},
"severity": {
"coding": [
{
"code": "24484000",
"system": "http://snomed.info/sct",
"display": "Severe"
}
]
},
"subject": {
"reference": "Patient/<id>"
},
"recordedDate": "2020-10-28"
}

{
"resourceType": "Condition",
"id": "chronic-comorbidity-absent",
"meta" : {
"profile" : [
"our_url_here"
]
},
"category": [
{
"coding": [
{
"code": "392521001",
"system": "http://snomed.info/sct",
"display": "History of (contextual qualifier) (qualifier value)"
}
]
}
],
"verificationStatus": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status",
"code": "refuted",
"display": "Refuted"
},
{
"system": "http://snomed.info/sct",
"code": "410594000",
"display": "Definitely NOT present (qualifier value)"
}
]
},
"code": {
"coding": [
{
"code": "709044004",
"system": "http://snomed.info/sct",
"display": "Chronic kidney disease (disorder)"
}
]
},
"subject": {
"reference": "Patient/<id>"
},
"recordedDate": "2020-10-28"
},

{
"resourceType": "Condition",
"id": "complication-present",
"meta" : {
"profile" : [
"our_url_here"
]
},
"category": [
{
"coding": [
{
"code": "116223007",
"system": "http://snomed.info/sct",
"display": "Complication (disorder)"
}
]
}
],
"code": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "14669001",
"display": "Acute renal failure syndrome (disorder)"
}
]
},
"verificationStatus": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status",
"code": "confirmed",
"display": "Confirmed"
},
{
"system": "http://snomed.info/sct",
"code": "410605003",
"display": "Confirmed present (qualifier value)"
}
]
},
"clinicalStatus": {
"coding": [
{
"code": "active",
"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
"display": "Active"
}
]
},
"subject": {
"reference": "Patient/<id>"
},
"recordedDate": "2020-10-15"
}
40 changes: 40 additions & 0 deletions fhir/resource_structure_dev/medication_administration.json
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{
"resourceType" : "MedicationAdministration",
"id" : "example",
"meta" : {
"profile" : [
"our_url_here"
]
},
"status" : "not-taken",
"medicationCodeableConcept" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "392327001",
"display" : "Azithromycin-containing product in oral dose form"
}
],
"text" : "Azithromycin"
},
"subject" : {
"reference" : "Patient/<id>",
"display" : "Eve Everywoman"
},
"encounter": {
"reference": "Encounter/<id>",
"display": "encounter_name"
},
"effectiveDateTime" : "2018-03-07",
"dosage" : {
"route" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "26643006",
"display" : "Oral route"
}
]
}
}
}
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