Proyecto IAI vaccines - Diplomado UTEC 2021

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Repositorio del Proyecto IAI vaccines titulado: "Aplicación de un modelo de aprendizaje no supervisado para la identificación de perfiles en riesgo de hospitalización por efectos adversos causados por la vacuna contra el Covid-19."

Integrantes:

1. Nicolle Pereira
2. David Guevera
3. Leidy Pola
4. Martina Guillermo
5. Angel Ramirez
6. Alvaro Rodríguez
7. Paulo Vela
8. Kathy Bolivar
9. Eduardo Apari

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Notas sobre el dataset VAERS

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About VAERS.

• The U.S. Department of Health and Human Services (DHHS) established VAERS, which is co-administered by the Food and Drug Administration (FDA) and the Centers for Disease Control (CDC), to accept all reports of suspected adverse events, in all age groups, after the administration of any U.S. licensed vaccine.
• The primary purpose for maintaining the database is to serve as an early warning or signaling system for adverse events not detected during pre-market testing.

Careful points about this data set

1. VAERS data are from a passive surveillance system and represent unverified reports of health events that occur after vaccination.
2. The event may have been related to an underlying disease or condition, to medications being taken concurrently, or may have occurred by chance.
3. VAERS data should be used with caution as numbers and conditions do not reflect data collected during follow-up.
4. Note that the inclusion of events in VAERS data does not infer causality.

About the data codification

• On 1/17/2007 the VAERS coding system was converted (from an older system: Coding Symbols for a Thesaurus of Adverse Reaction Terms (COSTART) used until 2007) to an international coding system that is used worldwide: Medical Dictionary for Regulatory Activities (MedDRA) which is more detailed.

MedDRA uses key words representing the medical condition(s) described in the case report and converts them to standardized codes. Here this dataset uses more than 17000 "Preferred Terms" MedDRA codes. Codes are updated semi-annually (here on COVID19, we have collected version 23.1 and 24.0).

About the data.

About 85-90% of vaccine adverse event reports concern relatively minor events, such as fevers or redness and swelling at the injection site. The remaining reports (less than 15%) describe serious events, such as hospitalizations, life-threatening illnesses, or deaths.

No data is provided that would allow identification of any individuals associated with these reports.

Data Collection: Based on 2 form versions, online version (on websites) and printing pdf version. Referred on the data set as (VAERS 1 and VAERS 2).

Structure: The downloadable VAERS public data set consists of 3 separate data files.

1. VAERSDATA.CSV - provides a detailed description of the data provided in each field.
2. VAERSVAX.CSV - provide the remaining vaccine information (vaccine name, manufacturer, lot number, route, site, and number of previous doses administered), for each of the vaccines listed. VAX_DOSE was discontinued in the VAERS 2 form.
3. VAERSSYMPTOMS.CSV - provide the adverse event coded terms utilizing the MedDRA dictionary. Each row in the .csv will contain up to 5 MedDRA terms per VAERS ID; thus, there could be multiple rows per VAERS ID. For each of the VAERS_ID’s listed in the VAERSDATA.CSV table, there is a matching record in this file, identified by VAERS_ID, Duplicates may appear in data and terms are listed in alphabetical order. In case a report has more than 5 terms multiple rows with 5 terms each will be listed for that VAERS ID.

Data Types

1. NUM (float64) = numeric data
2. CHAR (object) = text or "character" data
3. DATE (not formated) = date fields in mm/dd/yy format

Data sets merged (total 51 columns)

✔️	#	Column	Count	Dtype	Description	Notes	Options
✔️	#	VAERS_ID	591241	float64	VAERS Identification Number	Used for merging datasets	Unique for DB
✔️	0	RECVDATE	591241	Datetime	Date report was received		date
✔️	1	STATE	535248	object	State in the USA	2 letter code	nominal
✔️	2	AGE_YRS	558307	float64	Age in Years		integer
❌	3	CAGE_YR	510323	float64	Calculated age of patient in years	Needs summation	integer
❌	4	CAGE_MO	936	float64	Calculated age of patient in months	Needs summation	integer
✔️	5	SEX	591241	object	Sex		(M, F, Unknown=Blank)
❌	6	RPT_DATE	315	Datetime	Date Form Completed	REJECTED, low number records	date
🤖	7	SYMPTOM_TEXT	591181	object	Reported symptom text	In Review	text
✔️	8	DIED	9434	object	Died	Patient Outcomes	(Y, Blank)
✔️	9	DATEDIED	8835	Datetime	Date of Death	Patient Outcomes	date
✔️	10	L_THREAT	16254	object	Life-Threatening Illness	Patient Outcomes, Medical history	(Y, Blank)
❌	11	ER_VISIT	50	object	Emergency Room or Doctor Visit	Patient Outcomes VAERS 1 form only	(Y, Blank)
✔️	12	HOSPITAL	53726	object	Hospitalized	Patient Outcomes	(Y, Blank)
✔️	13	HOSPDAYS	39773	float64	Number of days Hospitalized	Patient Outcomes	integer
❌	14	X_STAY	418	object	Prolongation of Existing Hospitalization	Patient Outcomes	(Y, Blank)
✔️	15	DISABLE	13438	object	Disability	Patient Outcomes, Medical history	(Y, Blank)
✔️	16	RECOVD	541552	object	Recovered		(Y=recovered, N=not recovered, U=Blank)
✔️	17	VAX_DATE	564641	Datetime	Vaccination Date	Check here for vax dosage	date
✔️	18	ONSET_DATE	570860	Datetime	Adverse Event Onset Date	DOUBLE CHECK HERE	date
❌	19	NUMDAYS	548731	float64	Number of days (Onset date - Vax. Date)		integer
🤖	20	LAB_DATA	293299	object	Diagnostic laboratory data	Medical history
✔️	21	V_ADMINBY	591241	object	Type of facility where vaccine was administered		VAERS 1.0: PUB=Public, PVT=Private, MIL=Military, OTH=Other, UNK=Unknown. VAERS 2.0: ++ PHM=Pharmacy, SCH=school/student health clinic, SEN=Nursing home or senior living facility, WRK=Workplace clinic.
❌	22	V_FUNDBY	365	object	Type of funds used to purchase vaccines	VAERS 1 field only	PUB=Public, PVT=Private, MIL=Military; OTH=Other/Unknown
🤖	23	OTHER_MEDS	407792	object	Other Medications	Medical history	nominal
🤖	24	CUR_ILL	328851	object	Illnesses at time of vaccination	Medical history	nominal
🤖	25	HISTORY	422557	object	Chronic or long-standing health conditions	Medical history, VAERS 1 form only, this field also includes pre-existing physician-diagnosed allergies	nominal
🤖	26	PRIOR_VAX	36239	object	Prior Vaccination Event information	Medical history	nominal
❌	27	SPLTTYPE	98610	object	Manufacturer/Immunization Project Report Number	REJECTED, not on the scope	nominal
❌	28	FORM_VERS	591241	int64	VAERS form version 1 or 2	(1, 2)
❌	29	TODAYS_DATE	588302	Datetime	Date Form Completed	Not relevant REJECTED	date
❌	30	BIRTH_DEFECT	406	object	Congenital anomaly or birth defect	Patient Outcomes, Medical history. Only in VAERS2	(Y, Blank)
❌	31	OFC_VISIT	136672	object	Doctor or other healthcare provider office/clinic visit	Patient Outcomes,Only in VAERS2	(Y, Blank)
✔️	32	ER_ED_VISIT	103144	object	Emergency room/department or urgent care	Patient Outcomes,Only in VAERS2	(Y, Blank)
🤖	33	ALLERGIES	381752	object	Allergies to medications, food, or other products		nominal
❌	34	SYMPTOM1	591241	object	Adverse Event MedDRA Term 1		code
❌	35	SYMPTOMVERSION1	591241	float64	MedDRA dictionary version number 1		code
❌	36	SYMPTOM2	470315	object	Adverse Event MedDRA Term 2		code
❌	37	SYMPTOMVERSION2	470315	float64	MedDRA dictionary version number 2		code
❌	38	SYMPTOM3	367938	object	Adverse Event MedDRA Term 3		code
❌	39	SYMPTOMVERSION3	367938	float64	MedDRA dictionary version number 3		code
❌	40	SYMPTOM4	279936	object	Adverse Event MedDRA Term 4		code
❌	41	SYMPTOMVERSION4	279936	float64	MedDRA dictionary version number 4		code
❌	42	SYMPTOM5	207749	object	Adverse Event MedDRA Term 5		code
❌	43	SYMPTOMVERSION5	207749	float64	MedDRA dictionary version number 5		code
❌	44	VAX_TYPE	591241	object	Administered Vaccine Type		(Many, only COVID19 interested)
✔️	45	VAX_MANU	591241	object	Vaccine Manufacturer	important	(Many, only COVID19 interested)
✔️	46	VAX_LOT	419626	object	Manufacturer's Vaccine Lot	double check	(Many, only COVID19 interested)
✔️	47	VAX_DOSE_SERIES	588217	object	Number of doses administered	Not completely reliable, The VAERS 1 field VAX_DOSE was discontinued in the VAERS 2	(1 --if it was noted -- , Blank)
✔️	48	VAX_ROUTE	464076	object	Vaccination Route	Could be important..	(UN=Unknown, ID=Intradermal, IM=Intramuscular, SC=Subcutaneous, IN=Intranasal, PO=Per Oral, SYR=Needle and syringe (not specified further), JET=Needle free jet injector device,OT=Other)
✔️	49	VAX_SITE	476756	object	Vaccination [Anatomic] Site		nominal
❌	50	VAX_NAME	591241	object	Vaccination Name	REJECTED === VAX_MANU	(Many, only COVID19 interested)

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