043-covid

# COVID-19 dataset

Description

Information about Covid is collected in a standalone Covid survey and in the Follow-up Medical Survey in the Human Phenotype Project study.

Introduction

This Covid survey presents the participants with questions regarding their Covid-19 vaccinations and diagnosis status. It is asked in-person, in every visit to the clinical testing center. Questions asked are related to the participant’s vaccination status, number of vaccine doses and boosters, were participants diagnosed with Covid-19 in the past and were they hospitalized following diagnosis.

Measurement protocol

Participants are asked the COVID survey questions during the visit to the clinical testing center (CTC) both at baseline and on follow up visits. It is asked in person, and answers are filled into the system by study coordinators.

Data availability

The information is stored in 1 parquet file: covid.parquet. The ‘data source’ column indicates which survey the infromation comes from either the initial Covid survey or the Follow-up Medical Survey.

Relevant links

from pheno_utils import PhenoLoader

pl = PhenoLoader('covid')
pl

PhenoLoader for covid with
19 fields
2 tables: ['covid', 'age_sex']

Data dictionary

pl.dict

	folder_id	feature_set	field_string	relative_location	bulk_dictionary	bulk_file_extension	description_string	field_type	array	stability	units	sampling_rate	strata	sexed	debut	completed	pandas_dtype	data_coding
tabular_field_name
collection_timestamp	43	covid	Collection timestamp	covid/covid.parquet	NaN	NaN	Timestamp of measurements collection	Datetime	Single	Accruing	Time	NaN	Collection time	Both sexes	4/26/2021	NaN	datetime64[ns, Asia/Jerusalem]	NaN
collection_date	43	covid	Collection date	covid/covid.parquet	NaN	NaN	Date of measurments collection	Date	Single	Accruing	Time	NaN	Collection time	Both sexes	4/26/2021	NaN	datetime64[ns]	NaN
timezone	43	covid	Timezone	covid/covid.parquet	NaN	NaN	Timezone of the measurments	Categorical (single)	Single	Accruing	NaN	NaN	Collection time	Both sexes	4/26/2021	NaN	category	NaN
covid_vaccinated	43	covid	Were you vaccinated for Covid?	covid/covid.parquet	NaN	NaN	Were you vaccinated for Covid?	Categorical (single)	Single	Accruing	NaN	NaN	Primary	Both sexes	4/26/2021	NaN	int	7
covid_vaccination_doses_number	43	covid	Number of vaccine doses	covid/covid.parquet	NaN	NaN	Number of vaccine doses	Integer	Single	Accruing	NaN	NaN	Primary	Both sexes	4/26/2021	NaN	int	NaN
covid_vaccination_manufacturer	43	covid	Covid vaccine manufacture	covid/covid.parquet	NaN	NaN	Covid vaccine manufacture	Categorical (single)	Single	Accruing	NaN	NaN	Primary	Both sexes	4/26/2021	NaN	int	043_01
covid_vaccination_last_date	43	covid	Date of the last dose of Covid vaccine	covid/covid.parquet	NaN	NaN	Date of the last dose of Covid vaccine	Date	Single	Accruing	Time	NaN	Primary	Both sexes	4/26/2021	NaN	datetime64[ns]	NaN
covid_diagnosed	43	covid	Were you diagnosed with Covid	covid/covid.parquet	NaN	NaN	Were you diagnosed with Covid	Categorical (single)	Single	Accruing	NaN	NaN	Primary	Both sexes	4/26/2021	NaN	int	7
covid_diagnosed_date	43	covid	What was the date of diagnosis	covid/covid.parquet	NaN	NaN	What was the date of diagnosis	Date	Single	Accruing	Time	NaN	Primary	Both sexes	4/26/2021	NaN	datetime64[ns]	NaN
covid_symptoms	43	covid	Did you develop any symptoms	covid/covid.parquet	NaN	NaN	Did you develop any symptoms	Categorical (single)	Single	Accruing	NaN	NaN	Primary	Both sexes	4/26/2021	NaN	int	7
covid_hospitalization	43	covid	Were you hopitalized following your Covid diag...	covid/covid.parquet	NaN	NaN	Were you hopitalized following your Covid diag...	Categorical (single)	Single	Accruing	NaN	NaN	Primary	Both sexes	4/26/2021	NaN	int	7
covid_icu	43	covid	Were you hopitalized at the ICU following your...	covid/covid.parquet	NaN	NaN	Were you hopitalized at the ICU following your...	Categorical (single)	Single	Accruing	NaN	NaN	Primary	Both sexes	4/26/2021	NaN	int	7
covid_icu_days	43	covid	How many days did you spend in the ICU followi...	covid/covid.parquet	NaN	NaN	How many days did you spend in the ICU followi...	Integer	Single	Accruing	NaN	NaN	Primary	Both sexes	4/26/2021	NaN	int	NaN
covid_hospitalization_days	43	covid	How many days were you hospitalized	covid/covid.parquet	NaN	NaN	How many days were you hospitalized	Integer	Single	Accruing	NaN	NaN	Primary	Both sexes	4/26/2021	NaN	int	NaN
covid_oxygen	43	covid	Did you require oxygen following diagnosis wit...	covid/covid.parquet	NaN	NaN	Did you require oxygen following diagnosis wit...	Categorical (single)	Single	Accruing	NaN	NaN	Primary	Both sexes	4/26/2021	NaN	int	7
covid_invasive_respirator	43	covid	Did you require invasive respirator following ...	covid/covid.parquet	NaN	NaN	Did you require invasive respirator following ...	Categorical (single)	Single	Accruing	NaN	NaN	Primary	Both sexes	4/26/2021	NaN	int	7
data_source	43	covid	Data source	covid/covid.parquet	NaN	NaN	Source where data originates from	Text	Single	Accruing	NaN	NaN	Auxiliary	Both sexes	4/26/2021	NaN	string	NaN