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.
| 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
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.
| 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 |
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.
| 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
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