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Data_Items_Composition.md

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Covid

General queries

The following queries are used at the beginning of a run to determine the patient/encounter pool.

Retrieval input criteria

1) [base]/Condition?code=U07.1&_pretty=false&date=ge2020-01-27&_count=500
2) [base]/Observation?code=94640-0,94306-8,96763-8,94500-6,96895-8,96741-4&date=ge2020-01-27

Further data retrieval

3) [base]/Patient?_id=[ids_from_1_and_2]
4) [base]/Encounter?subject=[ids_from_3]&date=ge2020-01-27
5) [base]/Location?_id=[ids_from_4]
6) [base]/Procedure?code=26763009,243147009,[...],19647005&subject=[ids_from_1_and_2]

Data items composition

Most of the items just rely on data with at least one positive covid lab finding or diagnosis.

For all items that require the Versorgungsstellenkontakt, it is important that either the visit number (Encounter.identifier.value while Encounter.identifier.type.coding.code = VN is present in all encounters, or alternatively can be navigated through the hierarchy via Encounter.partOf (not recommended due to inefficiency).

Item name FHIR attributes Forced Condition Separation criterium
current.treatmentlevel Encounter.location referenced Location.type = ICU
Encounter.status IN-PROGRESS
Encounter.type Versorgungsstellenkontakt
Encounter.class IMP
Procedure.code code from VENTILATION/ECMO value set
Procedure.status IN-PROGRESS, FINISHED
current.maxtreatmentlevel Encounter.location referenced Location.type = ICU
Encounter.status IN-PROGRESS
Encounter.type Versorgungsstellenkontakt
Encounter.class IMP
Procedure.code code from VENTILATION/ECMO value set
current.age.maxtreatmentlevel.* Encounter.location referenced Location.type = ICU
Encounter.status IN-PROGRESS
Encounter.type Versorgungsstellenkontakt
Encounter.class IMP
Procedure.code code from VENTILATION/ECMO value set
Patient.birthDate
cumulative.results Observation.effective younger than kick-off-date
Observation.code IN (94640-0,94306-8,96763-8,94500-6)
Observation.valueCodeableConcept MII value set
cumulative.gender Patient.gender MII AdministrativeGender value set
cumulative.age Patient.birthDate
Encounter.period.start
cumulative.maxtreatmentlevel Encounter.location referenced Location.type = ICU
Encounter.type Versorgungsstellenkontakt IN-PROGRESS, FINISHED
Encounter.class IMP
Procedure.code code from VENTILATION/ECMO value set
cumulative.zipcode Patient.address.postalCode
Patient.address.country DE or not
cumulative.inpatient.gender Patient.gender MII AdministrativeGender value set
Encounter.class IMP
cumulative.outpatient.gender Patient.gender MII AdministrativeGender value set
Encounter.class AMB
cumulative.inpatient.age Patient.birthDate
Encounter.type Einrichtungskontakt
Encounter.period.start
Encounter.class IMP
cumulative.outpatient.age Patient.birthDate
Encounter.type Einrichtungskontakt
Encounter.period.start
Encounter.class AMB
cumulative.lengthofstay.icu.* Encounter.location referenced Location.type = ICU
Encounter.location.period / Encounter.period
Encounter.type Versorgungsstellenkontakt
Encounter.hospitalization.dischargeDisposition
.EntlassungsgrundErsteUndZweiteStelle		 07
cumulative.lengthofstay.hospital.* Encounter.type Einrichtungskontakt
Encounter.period
Encounter.hospitalization.dischargeDisposition
.EntlassungsgrundErsteUndZweiteStelle		 07
cumulative.varianttestresults Observation.effective younger than kick-off-date
Observation.code IN (96895-8,96741-4)
Observation.valueCodeableConcept Loinc codes from this value set
cumulative.age.maxtreatmentlevel.* Encounter.location referenced Location.type = ICU
Encounter.status IN-PROGRESS
Encounter.type Versorgungsstellenkontakt
Encounter.class IMP
Encounter.period.start
Procedure.code code from VENTILATION/ECMO value set
Patient.birthDate
timeline.tests Observation.effective younger than kick-off-date
Observation.code IN (94640-0,94306-8,96763-8,94500-6)
Observation.valueCodeableConcept MII value set
timeline.test.positive Observation.effective younger than kick-off-date
Observation.code IN (94640-0,94306-8,96763-8,94500-6)
Observation.valueCodeableConcept IN (10828004,260373001,52101004)
timeline.maxtreatmentlevel Encounter.location referenced Location.type = ICU
Encounter.location.period / Encounter.period
Encounter.type Versorgungsstellenkontakt
Encounter.class IMPor AMB
Procedure.code code from VENTILATION/ECMO value set
Procedure.period
timeline.varianttestresults Observation.effective younger than kick-off-date
Observation.code IN (96895-8,96741-4)
Observation.valueCodeableConcept Loinc codes from this value set
timeline.deaths Encounter.type Einrichtungskontakt
Encounter.class IMP
Encounter.period.end
Encounter.hospitalization.dischargeDisposition
.EntlassungsgrundErsteUndZweiteStelle		 07

Influenza

General queries

The following queries are used at the beginning of a run to determine the patient/encounter pool.

Retrieval input criteria

1) [base]/Condition?code=J10.0,J10.1,J10.8,J09&_pretty=false&date=ge2022-09-01&_count=500 
2) [base]/Observation?code=34487-9,60416-5,49521-8,49531-7,61365-3,48509-4,29909-9,40982-1&date=ge2022-09-01

Further data retrieval

3) [base]/Patient?_id=[ids_from_1_and_2]
4) [base]/Encounter?subject=[ids_from_3]&date=ge2022-09-01
5) [base]/Location?_id=[ids_from_4]
6) [base]/Procedure?code=26763009,243147009,[...],19647005&subject=[ids_from_1_and_2]

Data items composition

Most of the items just rely on data with at least one positive influenza lab finding or diagnosis.

Item name FHIR attributes Forced Condition Separation criterium
infl.current.treatmentlevel Encounter.location referenced Location.type = ICU
Encounter.status IN-PROGRESS
Encounter.type Versorgungsstellenkontakt
Encounter.class IMP
Procedure.code code from VENTILATION/ECMO value set
Procedure.status IN-PROGRESS, FINISHED
infl.current.maxtreatmentlevel Encounter.location referenced Location.type = ICU
Encounter.status IN-PROGRESS
Encounter.type Versorgungsstellenkontakt
Encounter.class IMP
Procedure.code code from VENTILATION/ECMO value set
infl.current.age.maxtreatmentlevel.* Encounter.location referenced Location.type = ICU
Encounter.status IN-PROGRESS
Encounter.type Versorgungsstellenkontakt
Encounter.class IMP
Procedure.code code from VENTILATION/ECMO value set
Patient.birthDate
infl.cumulative.results Observation.effective younger than kick-off-date
Observation.code IN (34487-9,60416-5,49521-8,49531-7,
61365-3,48509-4,29909-9,40982-1)
Observation.valueCodeableConcept MII value set
infl.cumulative.gender Patient.gender MII AdministrativeGender value set
infl.cumulative.age Patient.birthDate
Encounter.period.start
infl.cumulative.maxtreatmentlevel Encounter.location referenced Location.type = ICU
Encounter.type Versorgungsstellenkontakt IN-PROGRESS, FINISHED
Encounter.class IMP
Procedure.code code from VENTILATION/ECMO value set
infl.cumulative.zipcode Patient.address.postalCode
Patient.address.country DE or not
infl.cumulative.inpatient.gender Patient.gender MII AdministrativeGender value set
Encounter.class IMP
infl.cumulative.outpatient.gender Patient.gender MII AdministrativeGender value set
Encounter.class AMB
infl.cumulative.inpatient.age Patient.birthDate
Encounter.type Einrichtungskontakt
Encounter.period.start
Encounter.class IMP
infl.cumulative.outpatient.age Patient.birthDate
Encounter.type Einrichtungskontakt
Encounter.period.start
Encounter.class AMB
infl.cumulative.lengthofstay.icu.* Encounter.location referenced Location.type = ICU
Encounter.location.period
Encounter.location.physicalType wa
Encounter.type Versorgungsstellenkontakt
Encounter.hospitalization.dischargeDisposition
.EntlassungsgrundErsteUndZweiteStelle		 07
infl.cumulative.lengthofstay.hospital.* Encounter.type Einrichtungskontakt
Encounter.period
Encounter.hospitalization.dischargeDisposition
.EntlassungsgrundErsteUndZweiteStelle		 07
infl.cumulative.age.maxtreatmentlevel.* Encounter.location referenced Location.type = ICU
Encounter.status IN-PROGRESS
Encounter.type Versorgungsstellenkontakt
Encounter.class IMP
Encounter.period.start
Procedure.code code from VENTILATION/ECMO value set
Patient.birthDate
infl.timeline.tests Observation.effective younger than kick-off-date
Observation.code IN (34487-9,60416-5,49521-8,49531-7,
61365-3,48509-4,29909-9,40982-1)
Observation.valueCodeableConcept MII value set
infl.timeline.test.positive Observation.effective younger than kick-off-date
Observation.code IN (34487-9,60416-5,49521-8,49531-7,
61365-3,48509-4,29909-9,40982-1)
Observation.valueCodeableConcept IN (10828004,260373001,52101004)
infl.timeline.maxtreatmentlevel Encounter.location referenced Location.type = ICU
Encounter.location.period
Encounter.location.physicalType wa
Encounter.type Versorgungsstellenkontakt
Encounter.class IMPor AMB
Procedure.code code from VENTILATION/ECMO value set
Procedure.period
infl.timeline.deaths Encounter.type Einrichtungskontakt
Encounter.class IMP
Encounter.period.end
Encounter.hospitalization.dischargeDisposition
.EntlassungsgrundErsteUndZweiteStelle		 07

Kiradar

General queries

The following queries are used at the beginning of a run to determine the patient/encounter pool.

Retrieval input criteria

The codes are read dynamically from the application.yaml, all entries under global.inputcodes.kids-radar.kjp and global.inputcodes.kids-radar.rsv are read. The default list can be seen in the data set description.

1) [base]/Condition?code=J20.5,J21.0,J12.1,...,F98.9,F99&_pretty=false&_count=200

Further data retrieval

2) [base]/Patient?_id=[ids_from_1]
3) [base]/Encounter?subject=[ids_from_2]&date=gt2020-01-01&_class=IMP&_count=200

Data items composition

The following data items are generated for all patients who were under the age of 18 at the start of the treatment case and with at least one diagnosis per kiradar context (KJP or RSV). For the KJP data, encounters >18 years are also considered due to possible case merges (see dataset description).

To find out which encounters are valid, there are a few pre-filtering steps. In addition to age checks, which are also carried out again in the items due to clustering, the analysis of the condition diagnosis resources is mandatory. The necessary attributes are Condition.recordedDate and Condition.code.coding.code.

Item name FHIR attributes Forced Condition Separation criterium
kira.kjp.cumulative.diags.zipcode Patient.address.postalCode
Patient.address.country DE or not
kira.kjp.cumulative.diags.age Patient.birthDate
Encounter.type Einrichtungskontakt
Encounter.period.start
Encounter.class IMP
kira.kjp.cumulative.diags.gender Patient.gender
kira.kjp.cumulative.diags.lengthofstay Encounter.type Einrichtungskontakt
Encounter.period
kira.kjp.timeline.diags.occurrence Encounter.period.start
kira.rsv.cumulative.diags.zipcode Patient.address.postalCode
Patient.address.country DE or not
kira.rsv.cumulative.diags.age Patient.birthDate
Encounter.type Einrichtungskontakt
Encounter.period.start
Encounter.class IMP
kira.rsv.cumulative.diags.gender Patient.gender
kira.rsv.cumulative.diags.lengthofstay Encounter.type Einrichtungskontakt
Encounter.period
kira.rsv.timeline.diags.occurrence Encounter.period.start

Acribis

General queries

The acribis patient pool is determined on the basis of the consent resources.

Retrieval input criteria

The following fhir search queries are used:

1) [base]/Consent?category=https://www.medizininformatik-initiative.de/fhir/modul-consent/CodeSystem/mii-cs-consent-consent_category|2.16.840.1.113883.3.1937.777.24.2.184&date=ge2024-10-01

Further data retrieval

2) [base]/Encounter?subject=[ids_from_1]&date=ge2025-05-17T00:00:00&_class=IMP
3) [base]/Condition?encounter=[ids_from_2]
4) [base]/Procedure?encounter=[ids_from_2]
5) [base]/Patient?encounter=[ids_from_3_or_4]

Data items composition

The following attributes are checked to detect valid (acribis) consent resources:

Resource.attribute Forced Condition Separation criterium
Consent.category[0].system http://loinc.org
Consent.category[0].code 57016-8
Consent.category[1].system https://www.medizininformatik-initiative.de/fhir/modul-consent/CodeSystem/mii-cs-consent-consent_category
Consent.category[1].code 2.16.840.1.113883.3.1937.777.24.2.184
Consent.patient
Consent.policy urn:oid:2.16.840.1.113883.3.1937.777.24.2.1790 (any main form uri as 1.6d; 1.6f; 1.7.2...) or/and urn:oid:2.16.840.1.113883.3.1937.777.24.2.4031 (acribis)
Consent.provision.provision.type PERMIT
Consent.provision.provision.period.start >= 01.10.2024
Consent.provision.provision.code.system urn:oid:2.16.840.1.113883.3.1937.777.24.5.3
Consent.provision.provision.code.code 2.16.840.1.113883.3.1937.777.24.5.3.57

If additional special checks exist within the data items, these are listed here:

Item name FHIR attributes Forced Condition Separation criterium
acr.current.recruitment
acr.timeline.recruitment Consent.provision.provision.period.start
acr.current.dischargediags.cohorts Condition.code ICD codes from cohort logic
Procedure.code OPS codes from cohort logic
Encounter.diagnosis .use.coding.code = DD
acr.timeline.dischargediags.cohorts Condition.code ICD codes from cohort logic
Procedure.code OPS codes from cohort logic
Encounter.diagnosis .use.coding.code = DD