Transaction Bundle

The bundle of type 'transaction' is used to collect the set of resources as part of the GECCO dataset into a single instance for data exchange.


Profile - GECCO Bundle

Canonical: https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/gecco-bundle

Snapshot

idΣ0..1string
metaΣ0..1Meta
implicitRulesΣ ?!0..1uri
language0..1codeBinding
identifierΣ0..1Identifier
typeS Σ1..1codeBindingFixed Value
timestampS Σ0..1instant
totalΣ C0..1unsignedInt
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
relationΣ1..1string
urlΣ1..1uri
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
fullUrlΣ0..1uri
resourceΣ1..1Resource
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
modeΣ0..1codeBinding
scoreΣ0..1decimal
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
methodΣ1..1codeBinding
urlΣ1..1uri
ifNoneMatchΣ0..1string
ifModifiedSinceΣ0..1instant
ifMatchΣ0..1string
ifNoneExistΣ0..1string
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
statusΣ1..1string
locationΣ0..1uri
etagΣ0..1string
lastModifiedΣ0..1instant
outcomeΣ0..1Resource
signatureΣ0..1Signature


Profile - GECCO Bundle NUM-CODEX

This is a GECCO-Bundle for the NUM-CODEX use case. The bundle requires that at least a consent for data sharing is included. It is intended to use this bundle internally in the Data Sharing Framework. In contrast to the previous bundle, the type is set to 'batch'.

Canonical: https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/gecco-bundle-codex

Snapshot

idΣ0..1string
metaΣ0..1Meta
implicitRulesΣ ?!0..1uri
language0..1codeBinding
identifierΣ0..1Identifier
typeS Σ1..1codeBindingFixed Value
timestampS Σ0..1instant
totalΣ C0..1unsignedInt
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
relationΣ1..1string
urlΣ1..1uri
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
fullUrlΣ0..1uri
resourceΣ0..1Resource
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
modeΣ0..1codeBinding
scoreΣ0..1decimal
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
methodΣ1..1codeBinding
urlΣ1..1uri
ifNoneMatchΣ0..1string
ifModifiedSinceΣ0..1instant
ifMatchΣ0..1string
ifNoneExistΣ0..1string
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
statusΣ1..1string
locationΣ0..1uri
etagΣ0..1string
lastModifiedΣ0..1instant
outcomeΣ0..1Resource
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
fullUrlΣ0..1uri
resourceS Σ C1..1ConsentManagementConsent
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
modeΣ0..1codeBinding
scoreΣ0..1decimal
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
methodΣ1..1codeBinding
urlΣ1..1uri
ifNoneMatchΣ0..1string
ifModifiedSinceΣ0..1instant
ifMatchΣ0..1string
ifNoneExistΣ0..1string
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
statusΣ1..1string
locationΣ0..1uri
etagΣ0..1string
lastModifiedΣ0..1instant
outcomeΣ0..1Resource
signatureΣ0..1Signature


Examples

Bundle
Example bundle shortened for display purposes (uses literal references)

{
"resourceType": "Bundle",
"id": "gecco-bundle",
"meta": {
"profile": [
"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/gecco-bundle"
]
},
"type": "transaction",
"timestamp": "2020-11-10T15:50:41+01:00",
"entry": [
{
"fullUrl": "urn:uuid:b1128693-372d-469b-8288-04cf091e7553",
"resourceType": "Patient",
"id": "b1128693-372d-469b-8288-04cf091e7553",
"meta": {
"profile": [
"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/Patient"
]
},
{
"url": "https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/ethnic-group",
"code": "26242008",
"system": "http://snomed.info/sct",
"display": "Mixed (qualifier value)"
}
},
{
{
"url": "dateTimeOfDocumentation",
"valueDateTime": "2020-10-01"
},
{
"url": "age",
"value": 67,
"code": "a",
"system": "http://unitsofmeasure.org",
"unit": "years"
}
}
],
"url": "https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/age"
}
],
{
"type": {
"coding": [
{
"code": "MR",
"system": "http://terminology.hl7.org/CodeSystem/v2-0203"
}
]
},
"system": "https://www.charite.de/fhir/CodeSystem/medical-record-numbers",
"value": "43814872",
"reference": "Organization/Charité"
}
}
],
"birthDate": "1953-09-30"
},
"request": {
"method": "PUT",
"url": "Patient/b1128693-372d-469b-8288-04cf091e7553"
}
},
{
"fullUrl": "urn:uuid:8d4c2cbb-bc80-4e5a-82f0-0babf997660e",
"resourceType": "Condition",
"id": "8d4c2cbb-bc80-4e5a-82f0-0babf997660e",
"meta": {
"profile": [
"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/chronic-lung-diseases"
]
},
{
"coding": [
{
"code": "418112009",
"system": "http://snomed.info/sct",
"display": "Pulmonary medicine"
}
]
}
],
"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)"
}
]
},
"coding": [
{
"code": "active",
"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
"display": "Active"
}
]
},
"code": {
"coding": [
{
"code": "413839001",
"system": "http://snomed.info/sct",
"display": "Chronic lung disease"
}
]
},
"subject": {
"reference": "Patient/b1128693-372d-469b-8288-04cf091e7553"
},
"recordedDate": "2020-11-10T15:50:41+01:00"
},
"request": {
"method": "POST",
"url": "Condition"
}
},
{
"fullUrl": "urn:uuid:cabb511a-07be-4f2d-9444-54a4171a45a4",
"resourceType": "Observation",
"id": "cabb511a-07be-4f2d-9444-54a4171a45a4",
"meta": {
"profile": [
"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-rt-pcr"
]
},
{
"type": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "OBI"
}
]
},
"system": "https://www.charite.de/fhir/CodeSystem/lab-identifiers",
"value": "94500-6_SARS-CoV-2-RNA-Presence-in-Respiratory-specimen",
"reference": "Organization/Charité"
}
}
],
{
"coding": [
{
"system": "http://loinc.org",
"code": "26436-6"
},
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}
]
}
],
"code": {
"coding": [
{
"code": "94500-6",
"system": "http://loinc.org",
"display": "SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory specimen by NAA with probe detection"
}
],
"text": "SARS-CoV-2-RNA (PCR)"
},
"status": "final",
"subject": {
"reference": "Patient/b1128693-372d-469b-8288-04cf091e7553"
},
"effectiveDateTime": "2020-11-10T15:50:41+01:00",
"coding": [
{
"code": "260373001",
"system": "http://snomed.info/sct",
"display": "Detected (qualifier value)"
}
],
"text": "SARS-CoV-2-RNA positiv"
}
},
"request": {
"method": "PUT",
"url": "Observation/cabb511a-07be-4f2d-9444-54a4171a45a4"
}
}
]
}


Bundle
Example bundle as used in NUM-CODEX (uses logical references)

{
"resourceType": "Bundle",
"id": "gecco-bundle-num-codex",
"meta": {
"profile": [
"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/gecco-bundle-codex"
]
},
"type": "batch",
"entry": [
{
"fullUrl": "urn:uuid:dfd5edc6-3a8a-4796-a9bb-f9572cf15c96",
"resourceType": "Consent",
"id": "dfd5edc6-3a8a-4796-a9bb-f9572cf15c96",
"meta": {
"lastUpdated": "2021-05-19T17:50:23.000+02:00",
"profile": [
"http://fhir.de/ConsentManagement/StructureDefinition/Consent"
]
},
{
"url": "http://fhir.de/ConsentManagement/StructureDefinition/DomainReference",
{
"url": "domain",
"reference": "ResearchStudy/593d66f3-3654-4e8a-9524-3bcd78a363bb"
}
},
{
"url": "status",
"code": "active",
"system": "http://hl7.org/fhir/publication-status"
}
}
]
}
],
"status": "active",
"scope": {
"coding": [
{
"code": "research",
"system": "http://terminology.hl7.org/CodeSystem/consentscope"
}
]
},
{
"coding": [
{
"code": "57016-8",
"system": "http://loinc.org"
}
]
}
],
"patient": {
"reference": "Patient/c183799b-9fd8-416c-a826-e3c69a2a6c6d",
"display": "Pseudonym dic_charite/dic_C7H2E9"
},
"dateTime": "2021-05-19T00:00:00+02:00",
{
"display": "MII"
}
],
"reference": "QuestionnaireResponse/example"
},
"text": "Patienteneinwilligung MII|1.6.f"
},
"type": "deny",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "IDAT_bereitstellen_EU_DSGVO_konform",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy",
"display": "Herausgabe identifizierender Daten (IDAT)[...]"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.5",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "IDAT_erheben",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy",
"display": "Erfassung neuer identifizierender Daten (IDAT)"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.2",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "IDAT_speichern_verarbeiten",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy",
"display": "Speicherung und Verarbeitung identifizierender Daten (IDAT)[...]"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.3",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "IDAT_zusammenfuehren_Dritte",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy",
"display": "Zusammenführung identifizierender Daten (IDAT)[...]"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.4",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "MDAT_erheben",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy",
"display": "Erfassung medizinischer Daten"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.6",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "MDAT_speichern_verarbeiten",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy",
"display": "Speicherung_Verarbeitung von medizinischen Daten[...]"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.7",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "MDAT_wissenschaftlich_nutzen_EU_DSGVO_konform",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy",
"display": "Bereitstellung medizinischer Daten (MDAT)[...]"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.8",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "MDAT_zusammenfuehren_Dritte",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy",
"display": "Zusammenführung medizinischer Daten (MDAT)[...]"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.9",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "Rekontaktierung_Verknuepfung_Datenbanken",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy",
"display": "Rekontaktierung zur Verknüpfung[...]"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.27",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "Rekontaktierung_weitere_Erhebung",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy",
"display": "Rekontaktierung bezüglich Erhebung zusätzlicher Daten"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.28",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "Rekontaktierung_weitere_Studien",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy",
"display": "Rekontaktierung bezüglich Information[...]"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.29",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "MDAT_GECCO83_bereitstellen_NUM_CODEX",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy",
"display": "Medizinische Daten des GECCO83 Datensatz[...]"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.33",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "MDAT_GECCO83_speichern_verarbeiten_NUM_CODEX",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy",
"display": "Medizinische Daten des GECCO83 Datensatz[...]"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.34",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "MDAT_GECCO83_wissenschaftlich_nutzen_COVID_19_Forschung_EU_DSGVO_konform",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/MII",
"display": "Nutzung des Covid-19-Datensatzes[...]"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "MDAT_GECCO83_wissenschaftlich_nutzen_Pandemie_Forschung_EU_DSGVO_konform",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/MII",
"display": "Nutzung des Covid-19-Datensatzes[...]"
}
]
}
]
},
{
"type": "permit",
"period": {
"start": "2021-05-19T17:50:22+02:00",
"end": "2051-05-19T17:50:23+02:00"
},
"code": [
{
"coding": [
{
"code": "Rekontaktierung_Zusatzbefund",
"system": "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/MII",
"display": "Rekontaktierung bezüglich Zusatzbefund"
}
]
},
{
"coding": [
{
"code": "2.16.840.1.113883.3.1937.777.24.5.3.31",
"system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
}
]
}
]
}
]
}
},
"request": {
"method": "PUT",
"url": "Consent/dfd5edc6-3a8a-4796-a9bb-f9572cf15c96"
}
},
{
"fullUrl": "urn:uuid:c183799b-9fd8-416c-a826-e3c69a2a6c6d",
"resourceType": "Patient",
"id": "c183799b-9fd8-416c-a826-e3c69a2a6c6d",
"meta": {
"profile": [
"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/Patient"
]
},
{
"url": "https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/ethnic-group",
"code": "26242008",
"system": "http://snomed.info/sct",
"display": "Mixed (qualifier value)"
}
},
{
"url": "https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/age",
{
"url": "dateTimeOfDocumentation",
"valueDateTime": "2020-10-01"
},
{
"url": "age",
"value": 67,
"code": "a",
"system": "http://unitsofmeasure.org",
"unit": "years"
}
}
]
}
],
{
"type": {
"coding": [
{
"code": "ANON",
"system": "http://terminology.hl7.org/CodeSystem/v2-0203"
}
]
},
"system": "http://www.netzwerk-universitaetsmedizin.de/sid/dic-pseudonym",
"value": "dic_charite/dic_C7H2E9"
}
],
"birthDate": "1953-09-30"
},
"request": {
"method": "PUT",
"url": "Patient?identifier=http://www.netzwerk-universitaetsmedizin.de/sid/dic-pseudonym|dic_charite/dic_C7H2E9"
}
},
{
"fullUrl": "urn:uuid:12987d1f-7ce6-4d3a-993e-2cd553081092",
"resourceType": "Condition",
"id": "Inline-Instance-for-bundle-num-codex-example-1",
"meta": {
"profile": [
"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/chronic-lung-diseases"
]
},
{
"coding": [
{
"code": "418112009",
"system": "http://snomed.info/sct",
"display": "Pulmonary medicine"
}
]
}
],
"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)"
}
]
},
"coding": [
{
"code": "active",
"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
"display": "Active"
}
]
},
"code": {
"coding": [
{
"code": "413839001",
"system": "http://snomed.info/sct",
"display": "Chronic lung disease"
}
]
},
"subject": {
"system": "http://www.netzwerk-universitaetsmedizin.de/sid/dic-pseudonym",
"value": "dic_charite/dic_C7H2E9"
}
},
"recordedDate": "2020-11-10T15:50:41.000+01:00"
},
"request": {
"method": "PUT",
"url": "Condition?category=http://snomed.info/sct|418112009&code=http://snomed.info/sct|413839001&recorded-date=2020-11-10&subject:identifier=http://www.netzwerk-universitaetsmedizin.de/sid/dic-pseudonym|dic_charite/dic_C7H2E9"
}
}
]
}