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Data Dictionary v1

Authors: Esther Duflo¹, Nikhil Kanakamedala², Cyrus Graham Reginald², Ankit Agarwal², Jenny Wang¹, Karyn Real¹, Nick Foster³, Senthil Nachimuthu³, Josh Risley³, Ziad Obermeyer^3,4

¹ Massachusetts Institute of Technology
² Abdul Latif Jameel Poverty Action Lab
³ Nightingale Open Science
⁴ University of California, Berkeley

When using this resource, please cite: more options
Esther Duflo, Nikhil Kanakamedala, Cyrus Graham Reginald, Ankit Agarwal, Jenny Wang, Karyn Real, Nick Foster, Senthil Nachimuthu, Josh Risley, and Ziad Obermeyer. 2024. Multimodal Health Screening of Tamil Nadu Elders: A Nightingale Open Science Dataset. DOI:https://doi.org/10.48815/N50591

Additionally, please cite: more options
Sendhil Mullainathan and Ziad Obermeyer. 2022. Solving medicine’s data bottleneck: Nightingale Open Science. Nature Medicine 28, 5 (May 2022), 897–899. DOI:https://doi.org/10.1038/s41591-022-01804-4

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Table of contents

1. Participant Clinical Measurements and Survey Responses
2. Electrocardiograms
   1. 12 Lead ECG Waveforms
   2. Single Lead ECG Waveforms
3. Echocardiograms
   1. Echo Videos
   2. Echo Annotations
4. Fundus Images
5. Chest X-rays
   1. X-ray Images
   2. X-ray Annotation

File Tree

.
└── tamil-jpal-multi
    ├── echo
    │   ├── 00
    │   │   ├── 00ab...
    │   │   │   ├── 1.mpg
    │   ... ... ...
    │
    ├── ecg-12-lead
    │   └── waveform
    │       ├── 00
    │       │   ├── 00ab...npz
    │       ... ...
    │
    ├── ecg-single-lead
    │   ├── 00
    │   │   ├── 00ab...npz
    │   ... ... 
    │
    ├── fundus
    │   ├── 00
    │   │   ├── 00ab...
    │   │   │   ├── 1.jpg
    │   ... ... ...
    │
    ├── xray
    │   ├── 00
    │   │   ├── 00ab...jpg
    │   ... ... 
    │
    └── v1
        ├── patient-metrics.csv
        ├── echo-annotation.csv
        ├── echo-filepath.csv
        ├── ecg-12-lead-filepath.csv
        ├── ecg-single-lead-filepath.csv
        ├── fundus-filepath.csv
        ├── xray-annotation.csv
        └── xray-filepath.csv

Participant Clinical Measurements and Survey Responses

patient-metrics.csv contains the following medical data.

• Vitals - Blood Pressure, Pulse rate, Respiratory rate, SPO2
• Physical measures - Height, Weight, Waist/Hip/Mid-arm Circumference
• Fitness measures - Endurance test, Grip test
• Eye Measures - Tonometry, Fundus observations
• Cognition Score (MMSE short-form)
• Smoking Status responses
• Blood test data
• PHQ 4, Direct loneliness responses

Column Name	Description	Data Type	Example
patient_ngsci_id	Unique identifier for each respondent	string	24fc123…
year	Year of survey	int	2023
verbal_consent	Whether verbal consent was provided? Yes,No	string	Yes
age	Age of the respondent (value 999 represents age 90 and above)	int	60
sex	Sex of the respondent Female,Male	string	Female
bp	Whether bp was measured? Yes,No	string	Yes
bp_systolic, bp_diastolic	Blood pressure in mmHg	int	80
pulse	Whether pulse rate was measured? Yes,No	string	Yes
pulse_entry	Pulse rate in beats per min	int	83
resp_rate	Whether respiratory rate was measured? Yes,No	string	Yes
resp_rate_entry	Respiratory rate in breaths per min	int	22
spo2	Whether SPO2 was measured? Yes,No	string	Yes
spo2_entry	SPO2 level in %	float	98.0
rbs	Whether random blood sugar was measured? Yes,No	string	Yes
rbs_entry	Random blood sugar in mg/dL	float	138.0
height	Whether height was measured? Yes,No	string	Yes
height_entry	Height in cm	float	155.0
weight	Whether weight was measured? Yes,No	string	Yes
weight_entry	Weight in kg	float	60.0
midarm_circum	Whether MUAC was measured? Yes,No	string	Yes
midarm_circum_entry	Mid-arm circumference in cm	float	28.0
waist_circum	Whether waist circumference was measured? Yes,No	string	Yes
waist_circum_entry	Waist circumference in cm	float	88.0
hip_circum	Whether hip circumference was measured? Yes,No	string	Yes
hip_circum_entry	Hip circumference in cm	float	96.0
endurance_test	Whether endurance test was conducted? Yes,No	string	Yes
endurance_test_entry	Endurance test result in terms of no. of unassisted stands	int	11
grip_left, grip_right	Whether grip test was conducted, left and right hand? Yes,No	string	Yes
grip_left_entry, grip_right_entry	Grip test reading for left and right hand in kg	float	16.2
tonometry_lefteye, tonometry_righteye	Whether tonometry was conducted, left and right eye? Yes,No	string	Yes
tonometry_lefteye_entry, tonometry_righteye_entry	Tonometry reading for left and right eye in mmHg	float	17.3
fundus_lefteye, fundus_righteye	Whether the fundus examination was conducted, left and right eye? Yes,No	string	Yes
fundus_lefteye_obs, fundus_righteye_obs	Observations of the optometrist for left and right eye	string	…
cognition_sf	Whether MMSE short-form was conducted? Yes,No	string	Yes
cognition_sf_score	Score obtained on the MMSE short-form out of 16	int	13
cognit_impaired	Whether the MMSE short-form indicated cognitive impairment? Yes,No If the score is <8, the respondent has cognitive impairment	string	Yes
Hb	Hemoglobin in g/dl	float	12.3
HbA1c	HbA1c in %	float	6.0
triglycerides_mg_dl	Triglycerides Cholesterol in mg/dl	int	177
tot_cholesterol_mg_dl	Total Cholesterol in mg/dl	int	201
HDL_mg_dl	HDL Cholesterol in mg/dl	int	42
LDL_mg_dl	LDL Cholesterol in mg/dl	float	117.0
VLDL_mg_dl	VLDL Cholesterol in mg/dl	float	35.4
totchol_by_hdl_ratio	Total Cholesterol/HDL ratio	float	4.8
ldl_by_hdl_ratio	LDL/HDL ratio	float	2.77
creatinine_mg_dl	Serum Creatinine in mg/dl	float	0.9
literate	Whether the respondent is literate? Yes,No	string	Yes
smoking_1	Do you currently smoke tobacco on a daily basis, less than daily, or not at all? Daily,Less than daily,Not at all,Refused,Don’t know Source: GATS	string	Not at all
smoking_2	Have you smoked tobacco daily in the past? Yes,No,Refused,Don’t know Source: GATS	string	Yes
smoking_3	In the past, have you smoked tobacco on a daily basis, less than daily, or not at all? Daily,Less than daily,Not at all,Refused,Don’t know Source: GATS	string	Not at all
	The next four fields correspond to the responses of the 4-item patient health questionnaire on anxiety and depression. Source: PHQ-4 Over the last two weeks, how often have you been bothered by the following problems? Not at all,Several days,More than half the days,Nearly everyday,Refused,Don't know
phq_1	Feeling nervous, anxious or on edge	string	Not at all
phq_2	Not being able to stop or control worrying	string	Not at all
phq_3	Feeling down, depressed or hopeless	string	Not at all
phq_4	Little interest or pleasure in doing things	string	Not at all
direct_lonely	Over the last two weeks, how often have you been feeling lonely? Not at all,Several days,More than half the days,Nearly everyday,Refused	string	Several days

• Rows: 4,448
• Columns: 62

Electrocardiograms

This dataset contains electrocardiograms from two different devices. The first device produces a 12 lead ECG with a sample rate of 1000 Hz. The second device produces a single lead ECG with a sample rate of 300 Hz.

12 Lead ECG Waveforms

ecg-12-lead-filepath.csv

Column Name	Description	Data Type	Example
patient_ngsci_id	Unique identifier for each respondent	string	00ab…
filepath	Path to file	string	path/to/file

• Rows: 3,827
• Columns: 2

The ECG filepaths have the following structure:
ecg-12-lead/waveform/{first two digits of patient_ngsci_id}/{patient_ngsci_id}.npz

The waveform data for each ECG is stored in a separate compressed NumPy file. numpy.load doc. These files contain two arrays.

• 'waveform' - Raw waveform. Shape: (12, 10000)
• 'beat_waveform' - Beat waveform derived from the raw waveform data. Shape: (12, various)

Single Lead ECG Waveforms

ecg-single-lead-filepath.csv

Column Name	Description	Data Type	Example
patient_ngsci_id	Unique identifier for each respondent	string	00ab…
filepath	Path to file	string	path/to/file

• Rows: 4,224
• Columns: 2

The ECG filepaths have the following structure:
ecg-single-lead/{first two digits of patient_ngsci_id}/{patient_ngsci_id}.npz

The waveform data for each ECG is stored in a separate compressed NumPy file. numpy.load doc. These files contain two arrays.

• 'raw_waveform' - Raw waveform. Shape: (9000,)
• 'enhanced_waveform' - Enhanced waveform derived from the raw waveform data. Shape: (9000,)

Echocardiograms

Echo Videos

echo-filepath.csv

Column Name	Description	Data Type	Example
patient_ngsci_id	Unique identifier for each respondent	string	00ab…
echo_view	TTE views of video	int	1
video_format	The format of the video file	string	MPEG
filepath	Path to file	string	path/to/file

• Rows: 52,099
• Columns: 4

The echocardiogram videos are not uniformly formatted. There are three formats: AVI, MPEG, MP4. The filenames of the videos corresponds to one of 13 views, as seen below.

Transthoracic Echocardiography (TTE) Views

1. PSLAX: 2D
2. PSLAX: color (for assessing aortic and mitral regurgitation)
3. PSAX at AOV level: 2D
4. PSAX at AOV level: color
5. PSAX at MV level (visualize MV orifice)
6. PSAX at MV level: Color
7. PSAX at PAP level
8. Apical: Four-chamber: 2D (full visualization of atria and ventricles)
9. Apical: Four-chamber: color mitral regurgitation
10. Apical: Four-chamber: color tricuspid regurgitation
11. Apical: Five-chamber: color aortic regurgitation
12. Subcostal: 2D for interatrial septum
13. IVC: volume and IVC collapse

Acronyms: AOV, Aortic valve; MV, mitral valve; PAP, papillary muscle; PSAX, parasternal short-axis view; PSLAX, parasternal long-axis view; 2D, two-dimensional

Echo Annotations

echo-annotation.csv

The echocardiograms were reviewed by a cardiologist. The table contains the measurements preformed during the echo and the evaluation by the cardiologist.

Column Name	Description	Data Type	Example
patient_ngsci_id	Unique identifier for each respondent	string	00ab..
district_id	A number representing one of five districts	string	01
camp_id	A number representing a camp within the district	string	02
AO:cm	Aorta diameter [cm]	float	3.1
LA:cm	Left atrium diameter [cm]	float	3.9
PWD:cm	Left ventricular posterior wall thickness at end-diastole [cm]	float	0.9
PWS:cm	Left ventricular posterior wall thickness at end-systole [cm]	float	1.1
LVIDD:cm	Left ventricular internal dimension at end-diastole [cm]	float	4.2
LVIDS:cm	Left ventricular internal dimension at end-systole [cm]	float	2.6
IVSD:cm	Interventricular septum thickness at end-diastole [cm]	float	0.9
IVSS:cm	Interventricular septum thickness at end-systole [cm]	float	1.1
EF:%	Ejection Fracture [%]	int	63
FS:%	Fractional shortening [%]	int	33
SV:ml	Stroke volume [mL]	int	98
mitral_valve	An evaluation of the mitral valve	string	NORMAL
aortic_valve	An evaluation of the aortic valve	string	NORMAL
tricuspid_valve	An evaluation of the tricuspid valve	string	NORMAL
pulmonary_valve	An evaluation of the pulmonary valve	string	NORMAL
right_ventricle	An evaluation of the right ventricle	string	NORMAL
inter_ventricle_septum	An evaluation of the inter ventricle septum	string	NORMAL
inter_atrial_septum	An evaluation of the inter atrial septum	string	NORMAL
pulmonary_artery	An evaluation of the pulmonary artery	string	NORMAL
right_atrium	An evaluation of the right atrium	string	NORMAL
left_atrium	An evaluation of the left atrium	string	NORMAL
left_ventricle	An evaluation of the left ventricle	string	NORMAL
pericardium	An evaluation of the pericardium	string	NORMAL
clot/vegetation	An assessment of the presence of a clot or vegetation	string	NORMAL
impression	A general evaluation by the cardiologist	string	NO RWMA,NORMAL LV FUNCTION

Fundus Images

fundus-filepath.csv

Column Name	Description	Data Type	Example
patient_ngsci_id	Unique identifier for each respondent	string	00ab…
image_number	The image number	int	1
filepath	Path to file	string	path/to/file

• Rows: 18,445
• Columns: 3

Most patients have four images. The technicians were instructed to take and save four images per person in the following order: Left disc view, Left macular view, Right disc view, Right macular view.

Chest X-rays

X-ray Images

xray-filepath.csv

Column Name	Description	Data Type	Example
patient_ngsci_id	Unique identifier for each respondent	string	00ab…
filepath	Path to file	string	path/to/file

• Rows: 3,887
• Columns: 2

Patients will have at most one X-ray.

X-ray Annotation

xray-annotation.csv

Each patient’s X-ray has been review by a radiologist. The radiologist evaluated the X-ray in six categories and included an general impression of the X-ray.

Column Name	Description	Data Type	Example
patient_ngsci_id	Unique identifier for each respondent	string	00ab..
district_id	A number representing one of five districts	string	01
camp_id	A number representing a camp within the district	string	01
trachea	An evaluation of the trachea (windpipe)	string	Trachea appears normal
cardiothoracic	An evaluation of the Cardio-Thoracic Ratio, which is used to describe heart size	string	Cardiothoracic ratio is within normal limits
bilateral_lung	An evaluation of the lungs	string	Bilateral lung fields appear normal
costo	The costophrenic angle compares the angle between the diagram and the ribs.	string	Costo and cardiophrenic angles appear normal
visualised_bony	An evaluation of the bone structures	string	Visualised bony structures appear normal
extra_thoracic	An evaluation of soft tissue outside the chest cavity, e.g. breast tissue	string	Extra thoracic soft tissues shadow grossly appears normal
xray_impression	A general evaluation of the X-ray from the radiologist	string	Chest X-ray shows no significant abnormality