COVID-19
Analysis of high resolution clinical data for COVID-19 patients could significantly impact guidelines around optimal treatment.
Due to significant administrative challenges in sharing de-identified clinical data, we have created a repository for performing federated analysis of COVID-19 patients.
The idea is simple: reformat your data into our proposed 10-15 views, and you'll be able to leverage all analysis code in this repository.
We are actively seeking collaborators to expand the scope of the analysis to more patients!
Organization
The organization is as follows:
-
sql - The SQL folder has local scripts for each dataset which convert.
-
mimic-iii - MIMIC-III is a publicly accessible critical care database. Though MIMIC-III does not contain information on patients with COVID-19, its highly accessible nature makes it useful for prototyping. The MIMIC-III Clinical Database Demo is openly available and can be used to better understand the queries and ultimate data structure.
-
mimic-iv - MIMIC-IV is a non-public update to MIMIC-III which contains more recent information.
-
data - A placeholder folder to contain harmonized datasets. Analysis code assumes data is present in this folder.
-
notebooks - Jupyter notebooks which contain end-to-end analyses of COVID-19 data.
Table structure
In order to facilitate shared analysis, we have defined a common set of views/tables.
The table structure is a work in progress.
| Table |
Content |
| cohort |
Defines stay_id, a single ICU stay. |
| vitalsign |
Glasgow coma scale measures. |
| gcs |
Glasgow coma scale measures. |
| rass |
Richmond Sedation Agitation Scale measurements |
| oxygen_delivery |
Information regarding supplemental oxygen delivery |
| ventilator_setting |
Measurements and settings associated with non-invasive and invasive mechanical ventilation |
| vitalsign |
Nurse validated vital sign measurements |
| vasopressor |
Administration and dose of intravenous vasopressors |
| bg |
Blood gas measurements |
| cbc |
Counts of the number of blood cells and related measures. |
| differential |
Detailed differential counts of white blood cells |
| red cell morphology |
Morphology of red blood cells |
| coagulation |
Measures of blood coagulation |
| chemistry |
Electrolyte and protein counts |
| enzymes |
Enzymes concentrations and bilirubin concentration |
| cardiac_markers |
Markers of cardiac function or injury |
| inflammation_measures |
Measures of inflammation |
Detailed tables
Cohort
Must create a stay_id, intime, outtime triplet to assign a unique stay in the ICU for each patient. subject_id should uniquely define the patient.
Charted data
Vital signs
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| charttime |
Timestamp |
N/A |
Time at which the charted event was valid. |
| heart_rate |
NUMERIC |
Beats per minute |
Number of heart beats per minute. |
| sbp |
NUMERIC |
mmHg |
Systolic blood pressure. |
| dbp |
NUMERIC |
mmHg |
Diastolic blood pressure. |
| mbp |
NUMERIC |
mmHg |
Mean blood pressure. |
| sbp_ni |
NUMERIC |
mmHg |
Non-invasively recorded systolic blood pressure. |
| dbp_ni |
NUMERIC |
mmHg |
Non-invasively recorded diastolic blood pressure. |
| mbp_ni |
NUMERIC |
mmHg |
Non-invasively recorded mean blood pressure. |
| resprate |
NUMERIC |
Breaths per minute |
Respiratory rate. |
| temperature |
NUMERIC |
Degrees Celsius |
Patient body temperature. |
| temperature_site |
NUMERIC |
N/A |
Site at which the measurement is taken. |
| spo2 |
NUMERIC |
% (percentage) |
Peripheral oxygen saturation. |
| glucose |
NUMERIC |
mg/dL |
Serum glucose measured using a fingerstick. |
GCS
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| charttime |
Timestamp |
N/A |
Time at which the charted event was valid. |
| gcs |
Integer |
N/A |
Glasgow coma scale. |
| gcs_motor |
Integer |
N/A |
|
| gcs_verbal |
Integer |
N/A |
|
| gcs_eyes |
Integer |
N/A |
|
| gcs_unable |
Integer |
N/A |
Unable to assess GCS due to sedation/intubation. |
RASS
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| stay_id |
Integer |
N/A |
Encounter identifier. |
| charttime |
Timestamp |
N/A |
Time at which the charted event was valid. |
| rass |
Integer |
N/A |
Current Richmond Agitation Sedation Scale value |
| rass_target |
Integer |
N/A |
Desired Richmond Agitation Sedation Scale value |
Oxygen Delivery
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| charttime |
Timestamp |
N/A |
Time at which the charted event was valid. |
| o2_flow |
Numeric |
Litres/minute |
Oxygen flow provided to the patient. |
| o2_flow_additional |
Numeric |
Litres/minute |
Additional oxygen flow provided by one or more secondary devices. |
| o2_delivery_device_1 |
Numeric |
N/A |
Primary oxygen delivery device. |
| o2_delivery_device_2 |
Numeric |
N/A |
Secondary oxygen delivery device. |
| o2_delivery_device_3 |
Numeric |
N/A |
Tertiary oxygen delivery device. |
| o2_delivery_device_4 |
Numeric |
N/A |
Quartenary oxygen delivery device. |
Ventilator Setting
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| charttime |
Timestamp |
N/A |
Time at which the charted event was valid. |
| respiratory_rate_set |
Numeric |
Breaths/min |
Breathing rate set by the ventilator |
| respiratory_rate_spontaneous |
Numeric |
Breaths/min |
Breathing rate occuring above the set rate |
| respiratory_rate_total |
Numeric |
Breaths/min |
Actual breathing rate |
| minute_volume |
Numeric |
L/min |
Litres of air inspired per minute |
| tidal_volume_set |
Numeric |
mL |
Tidal volume set by the ventilator |
| tidal_volume_observed |
Numeric |
mL |
Observed tidal volume |
| tidal_volume_spontaneous |
Numeric |
mL |
Tidal volume of spontaneous breaths over the ventilator |
| plateau_pressure |
Numeric |
cm H2O |
Maximum pressure observed in the lungs |
| peep |
Numeric |
cm H2O |
Positive end expiratory pressure |
| fio2 |
Numeric |
Proportion |
Fraction of inspired oxygen in the air |
| ventilator_mode |
String |
N/A |
Mode of ventilation (assist control, etc) |
| ventilator_mode_hamilton |
String |
N/A |
Special mode settings for Hamilton brand ventilators |
| ventilator_type |
String |
N/A |
Type of ventilator used |
Labs
Blood gases
Laboratory measures from patients with the time of blood collection and the time at which the result was available.
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| charttime |
Timestamp |
N/A |
Time at which the specimen was drawn from the patient. |
| specimen_id |
Integer |
N/A |
Unique identifier for the specimen drawn from the patient which the measurements are derived from. |
| Temperature |
Numeric |
|
|
| so2 |
Numeric |
|
|
| pO2 |
Numeric |
|
|
| pCO2 |
Numeric |
|
|
| pH |
Numeric |
|
|
| aado2 |
Numeric |
|
|
| pafi |
Numeric |
|
|
| calTCO2 |
Numeric |
|
|
| Base Excess |
Numeric |
|
|
| hematocrit |
Numeric |
|
|
| hemoglobin |
Numeric |
|
|
| carboxyhemoglobin |
Numeric |
|
|
| methemoglobin |
Numeric |
|
|
| chloride |
Numeric |
|
|
| calcium |
Numeric |
|
|
| potassium |
Numeric |
|
|
| sodium |
Numeric |
|
|
| lactate |
Numeric |
|
|
| glucose |
Numeric |
|
|
complete_blood_count
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| charttime |
Timestamp |
N/A |
Time at which the specimen was drawn from the patient. |
| specimen_id |
Integer |
N/A |
Unique identifier for the specimen drawn from the patient which the measurements are derived from. |
| hct |
Numeric |
% |
Hematocrit |
| hgb |
Numeric |
g/dL |
Hemoglobin |
| mch |
Numeric |
pg |
Mean corpuscular hemoglobin |
| mchc |
Numeric |
g/dL |
Mean corpuscular hemoglobin concentration |
| mcv |
Numeric |
fL |
Mean corpuscular volume |
| platelets |
Numeric |
K/uL |
Platelet count |
| rbc |
Numeric |
m/uL |
Red blood cells |
| rdw |
Numeric |
% |
Red blood cell distribution width |
| rdwsd |
Numeric |
fL |
Red blood cell distribution width standard deviation |
| wbc |
Numeric |
K/uL |
White blood cell count |
differential
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| charttime |
Timestamp |
N/A |
Time at which the specimen was drawn from the patient. |
| specimen_id |
Integer |
N/A |
Unique identifier for the specimen drawn from the patient which the measurements are derived from. |
| specimen_type |
Text |
|
|
| abs_basophils |
Numeric |
K/uL |
Absolute Basophil Count |
| abs_eosinophils |
Numeric |
K/uL |
Absolute Eosinophil Count |
| abs_lymphocytes |
Numeric |
K/uL |
Absolute Lymphocyte Count |
| abs_monocytes |
Numeric |
K/uL |
Absolute Monocyte Count |
| abs_neutrophils |
Numeric |
K/uL |
Absolute Neutrophil Count |
| atyps |
Numeric |
% |
Atypical Lymphocytes |
| bands |
Numeric |
% |
Immature Band Forms |
| imm_granulocytes |
Numeric |
% |
Immature Granulocytes |
| metas |
Numeric |
% |
Metamyelocytes |
| nrbc |
Numeric |
% |
Nucleated Red Blood Cells |
red_cell_morphology
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| charttime |
Timestamp |
N/A |
Time at which the specimen was drawn from the patient. |
| specimen_id |
Integer |
N/A |
Unique identifier for the specimen drawn from the patient which the measurements are derived from. |
| rbc morph |
Numeric |
|
|
| poiklo |
Numeric |
|
|
| polychr |
Numeric |
|
|
| ovalocy |
Numeric |
|
|
| target |
Numeric |
|
|
| cshisto |
Numeric |
|
|
| echino |
Numeric |
|
|
coagulation
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| charttime |
Timestamp |
N/A |
Time at which the specimen was drawn from the patient. |
| specimen_id |
Integer |
N/A |
Unique identifier for the specimen drawn from the patient which the measurements are derived from. |
| d_dimer |
Numeric |
ng/mL FEU |
D-Dimer |
| fibrinogen |
Numeric |
mg/dL |
Fibrinogen, Functional |
| thrombin |
Numeric |
sec |
Thrombin Time |
| inr |
Numeric |
N/A (ratio) |
International Normalized Ratio |
| pt |
Numeric |
sec |
Prothrombin Time |
| ptt |
Numeric |
sec |
Partial Thromboplastin Time |
chemistry
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| charttime |
Timestamp |
N/A |
Time at which the specimen was drawn from the patient. |
| specimen_id |
Integer |
N/A |
Unique identifier for the specimen drawn from the patient which the measurements are derived from. |
| Albumin |
Numeric |
g/dL |
|
| Globulin |
Numeric |
g/dL |
|
| total_protein |
Numeric |
g/dL |
|
| aniongap |
Numeric |
mEq/L |
|
| bicarbonate |
Numeric |
mEq/L |
|
| bun |
Numeric |
mg/dL |
|
| calcium |
Numeric |
mg/dL |
|
| chloride |
Numeric |
mEq/L |
|
| creatinine |
Numeric |
mg/dL |
|
| glucose |
Numeric |
mg/dL |
|
| sodium |
Numeric |
mEq/L |
|
| potassium |
Numeric |
mEq/L |
|
Enzymes (and Bilirubin)
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| charttime |
Timestamp |
N/A |
Time at which the specimen was drawn from the patient. |
| specimen_id |
Integer |
N/A |
Unique identifier for the specimen drawn from the patient which the measurements are derived from. |
| alt |
Numeric |
|
Alanine Aminotransferase |
| alkphos |
Numeric |
|
Alkaline Phosphatase |
| ast |
Numeric |
|
Asparate Aminotransferase |
| amylase |
Numeric |
|
Amylase |
| bilirubin_total |
Numeric |
|
Total Bilirubin (direct + indirect) |
| bilirubin_direct |
Numeric |
|
Direct Bilirubin |
| bilirubin_indirect |
Numeric |
|
Indirect Bilirubin |
| ck_cpk |
Numeric |
|
Creatinine Kinase |
| ld_ldh |
Numeric |
|
Lactate Dehydronase. |
Cardiac Markers
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| charttime |
Timestamp |
N/A |
Time at which the specimen was drawn from the patient. |
| specimen_id |
Integer |
N/A |
Unique identifier for the specimen drawn from the patient which the measurements are derived from. |
| troponin_i |
Numeric |
|
Troponin I |
| troponin_i_poc |
Numeric |
|
Troponin I, Point of Care test |
| troponin_t |
Numeric |
|
Tropinin T |
| ck_mb |
Numeric |
|
Creatinine Kinase, MB Isoenzyme |
Inflammation measures
| Column |
Data type |
Unit of measure |
Description |
| subject_id |
Integer |
N/A |
Patient identifier. |
| charttime |
Timestamp |
N/A |
Time at which the specimen was drawn from the patient. |
| specimen_id |
Integer |
N/A |
Unique identifier for the specimen drawn from the patient which the measurements are derived from. |
| crp |
Numeric |
|
C-reactive Protein |
| crp_high_sens |
Numeric |
|
C-reactive Protein, high sensitivity assay |
| il6 |
Numeric |
|
Interleukin-6 (send out) |
| procalcitonin |
Numeric |
|
Procalcitonin |
hematologic/other
- ferritin
- ggt
- transaminase
- 5ntd
- ceruloplasmin
- alpha-fetoprotein
COVID-19 copied to clipboard
MIT-LCP
MIT-LCP