MIT-LCP / COVID-19

Analysis of high resolution clinical data for COVID-19 patients

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