SICdb Documentation

Introduction

he SICdb dataset provides insight to over 27 thousand intensive care admissions, including therapy and data of their preceding surgery. Data was collected between 2013 and 2021 from 4 of the intensive care units at the University Hospital Salzburg, having more than 3 thousand intensive care admissions per year on 37 beds. The dataset is deidentified and contains, amongst others, case information, laboratory, medication, monitor and respirator signal data.SICdb provides aggregated once-per-hour and highly granular once-per-minute data.

File Description

The SICdb dataset consists of 8 files. All data files in the SICdb dataset are provided as comma seperated files (.csv) using the RFC 4180 standard. Additionally all files are compressed with gzip, an commonly used openly available compression method.

List of files

"The "cases" table is the base table of the SICdb dataset and the "CaseID" field serves as the identifier that relates all data. Each admission to the intensive care unit generates a unique "CaseID." To identify readmissions, a "PatientID" is provided. The "OffsetAfterFirstAdmission" field stores the time between the first admission and the current one.

"TimeOfStay" is the time in seconds from the admission recorded by the MetaVision system to the discharge. This time may include any preceding surgery and ends when the case is closed.

There are three fields indicating survival: "DischargeState" indicates the patient's state upon discharge from the ICU and is taken from the MetaVision discharge form. "HospitalDischargeType" provides information on how the case was closed in the clinical information system. "OffsetOfDeath" is the time in seconds from admission to death and includes additional hospital stays and out of hospital mortality. As it refers to a 1-year mortality it is set to null if death occurred more than one year after admission.

cases.csv.gz

Name	Type	Description	Comment
CaseID	Integer	A randomly assigned identifier	CaseID is unique to each admission.
PatientID	Integer	A randomly assigned identifier	PatientID is unique to each Patient, useful to identify readmission
AdmissionYear	Integer	Year of admission
TimeOfStay	Integer	Time of stay (seconds)	Time from primary metavision admission, to last discharge. In cases, where the patient is admitted to ward after surgery, this will include surgery time.
ICUOffset	Integer	Time of actual ICU admission	SICdb includes preceding surgery if applicable, this field indicates the first transfer to an intensive or intermediate care ward
saps3	Float	Simplified Acute Physiology Score III
HospitalDischargeType	Reference	Type of hospital discharge.	This field indicates survival.
HospitalDischargeDay	Integer	The day of hospital discharge after admission	Note that this data is only available in days
HospitalStayDays	Integer	Days stayed in hospital for this case, including pre icu.
DischargeState	Reference	Type of icu discharge	This field indicates survival on icu
DischargeUnit	Reference	Unit the patient was discharged to, as selected in Metavision discharge form
OffsetOfDeath	Integer	1-year mortality in seconds from primary admission to death	1 year mortality, including out-of-hospital as far as known. See The "OffsetOfDeath" field denotes the elapsed time, in seconds, from admission to death, taking into account any subsequent hospital stays and out-of-hospital mortality data. The data was gathered from various sources, including government data. It is set to null if the death occurs more than one year after admission, since it is defined to 1-year mortality. For technical reasons observation time is only 6 month for some patients, field "EstimatedSurvivalObservationTime" holds information about that. However, it is worth noting that in some cases, if a patient dies in foreign countries, the information may be scarce. Postal address validity checks were performed, but no statistically significant differences were found, indicating that this may not be an issue of concern. for further information.
EstimatedSurvivalObservationTime	Reference	Estimation of oversation time, either 1-year or 6-month
Sex	Reference
WeightOnAdmission	Float	Rounded to +-5kg
HeightOnAdmission	Float	Rounded to +-5cm
AgeOnAdmission	Integer	Rounded to +-5y, over 90 set to 90
HospitalUnit	Reference	Last unit using this case
ReferringUnit	Reference	Referring unit as selected in admission form	Note: Unfortunatly in some cases "Notaufnahme" is selected here, so the referring unit is not specified in these cases.
ICD10Main	Text	ICD10 main code
ICD10MainText	Text	ICD10 main text
SurgicalSite	Reference
InterventionsText	Text	List of interventions
HoursOfCRRT	Integer	Hours of continuous renal replacement threapy this admission **
AdmissionFormHasSepsis	Reference	A mandatory field in the admission form **
HeartSurgeryAdditionalData	For heart surgery patients there is additional data collected **	Yes if applicable
HeartSurgeryCPBTime	Integer	Bypass time **
HeartSurgeryBeginOffset	Integer	Offset in seconds from ICU admission to cut **
HeartSurgeryEndOffset	Integer	Offset in seconds from ICU admission to end of surgery**
OffsetAfterFirstAdmission	Integer	If a patient has more than one admission, this is the offset in seconds from the first

* These fields are not available on PhysioNet at the moment. Contact us for further information.
** These fields will be moved to data tables in version 1.1.0

Data Description d_references

The d_references table contains information on all encoded data fields of the SICdb dataset. Each field, that has "Reference" as field type, is associated with the ReferenceGlobalID in the d_references table. Additionally ReferenceUnit describes the unit of measurement used for this field. Refer to chapter SQL Examples to learn how to easily use this table in relational databases.

d_references.csv.gz

Name	Type	Description	Comment
ReferenceGlobalID	Integer	The unique ID for the reference	Use this identifier as dictionary for alle encoded fields
ReferenceValue	Text	Reference value	i.e. "Creatinine"
ReferenceName	Text	The name of the reference	i.e. "Laboratory"
ReferenceUnit	Text	The unit of this item if applicable	i.e. "mg/dl"
LOINC_code	Text	LOINC Code
LOINC_short	Text	LOINC SHORTNAME
LOINC_long	Text	LOINC LONG_COMMON_NAME

Data Description data_float_h

Contains hourly float data associated with a case. If more (minute) data is available, data was aggregated and the corresponding values are stored in rawdata field. Refer to Deserialize Raw Data for more information. Metavision does, in database, not differentiate between qualitative (i.e. blood pressure) and quantitative (i.e. drainage volume) data, this was done programatically saving the sum instead of average. The field cnt indicates the amount of values aggregated.

data_float_h.csv.gz

Name	Type	Description	Comment
CaseID	Integer	Case identifier
DataID	Reference
Offset	Integer	Time in seconds after admission
Val	Float	Value	The unit (if applicable) is found in d_references where data_float_h.DataID is associated to d_references.ReferenceGlobalID
cnt	Integer	Amount of values aggregated
rawdata	Blob	List of 60 floats containing raw data	Due to excessive storage needs minute values have been aggregated.

Refer to chapter "Decode raw_data" for more information

Data Description data_ref

data_ref.csv.gz contains referenced (nominal) data and is unique per icu admission.

data_ref.csv.gz

Name	Type	Description	Comment
id	Integer	Primary Key
CaseID	Integer	Case identifier
FieldID	Reference	Refers to the name of the field	i.e. PreconditionDiabetes
RefID	Reference

Data Description laboratory.csv.gz

The laboratory table contains all available lab data, in many cases including the pre-admission labs.

Like all "Reference" fields additional data like name and unit of measurement is found in d_references. See SQL Examples to learn how to connect them using a relational database system.

To simplify lookup for labs of previous stays PatientID was added to this table.

laboratory.csv.gz

Name	Type	Description	Comment
id	Integer	Primary Key
CaseID	Integer	Case identifier
PatientID	Integer	Patient identifier
DrugID	Reference
Offset	Integer	Time in seconds after admission
LaboratoryValue	Float	Value	Unity of measurement can be found in d_references
LaboratoryType	Reference	Used for special laboratory types, i.e. arterial blood gas.

Preprocessed fields

Processed_Referenced_Fields

Version Information

The SICdb dataset uses a versioning system. It contains 3 numbers major, minor and patch. A suffix may be added for changes, the do not necessarily needs to be applied.

A major version change generally occurs when the database was incrementally updated and more cases are included.

A minor version change occurs when data was altered that will likely change most study data. (i.e. removal of a significant amount of invalid cases) A minor update also applies when new data is added (i.e. a new table) but the existing data is not altered.

A patch version change occurs when only specific data was altered and will not affect all exports. Please read changelog to check if your data is affected.

1.0.8 (07/2024)

• Added LOINC codes to laboratory references

1.0.7 (04/2024)

• Added field `cases`.`HospitalDischargeDay` `HospitalStayDays` representing the day of release from hospital after admission and the full lenght of hospital stay, respectively.
• Added field `cases`.`AdmissionUrgency`, depicting the urgency of admission
• Added High Flow (HFNC) therapy data
• Added Richmond Agitation-Sedation Scale (RASS) score
• Added Numeric Rating Scale (NRS-11) 
• Added SOFA Score
• Removed 36 invalid cases
• Recalculated field `cases`.`OffsetAfterFirstAdmission`, fixing an issue that occasionally led to inadequate values

1.0.6 (05/2023)

• [Important] Update a major error at the heart rate signal (invalid mapping of ecg signal)
• [Important] Renamed heart rate signals
• [Important] Updated some (~150) invalid weight/height signals
• [Fix] Due to a change in table structure the Premedication_ fields missed reference id, fixed
• Added KDIGO_AKI_168 and published algorithm (note: in general be careful with using urine output KDIGO in automated datasets)
• Added field ICUOffset for better comparability with other ICU datasets
• Added more signal data
• Corrected a small issue in the norepinephrine per kg algorithm (change is not significant)

1.0.5

• Merged additional mortality data and changed OffsetOfDeath from in-hospital-mortality to general 1-year-mortality
• Removed or fixed 190 cases of inplausible height or weight data
• Added some more CRRT data
• Recalculated DrainageSum

1.0.4

• Added unity of measurements for signal data
• Structural changes