Loading VAERS data into Postgres

For those who want to load VAERS data into Postgres, here's how I did it.

In case you have technical questions -> twitter: @waukema. 

/*

DROP TABLE vaers.symptoms;

CREATE TABLE vaers.symptoms

(

  id serial NOT NULL,

  vaers_id char(7),

  symptom1 character varying,

  symptomversion1 numeric,

  symptom2 character varying,

  symptomversion2 numeric,

  symptom3 character varying,

  symptomversion3 numeric,

  symptom4 character varying,

  symptomversion4 numeric,

  symptom5 character varying,

  symptomversion5 numeric

)

WITH (

  OIDS=FALSE

);

--msdos windows server 2008 postgres 9.3 using gnuwin32 utils:

--cat 2021VAERSSYMPTOMS.csv|psql -h localhost -d postgres -a -c "set client_encoding=latin1; copy vaers.symptoms (VAERS_ID, SYMPTOM1, SYMPTOMVERSION1, SYMPTOM2, SYMPTOMVERSION2, SYMPTOM3, SYMPTOMVERSION3, SYMPTOM4, SYMPTOMVERSION4, SYMPTOM5, SYMPTOMVERSION5) from stdin delimiter ',' CSV HEADER"

create table vaers.allsymptoms as

(

select 

vaers_id,

symptom1 as symptom,

symptomversion1 as symptomversion

from 

vaers.symptoms

where

symptom1 is not null

union all

select 

vaers_id,

symptom2 as symptom,

symptomversion2 as symptomversion

from 

vaers.symptoms

where

symptom2 is not null

union all

select 

vaers_id,

symptom3 as symptom,

symptomversion3 as symptomversion

from 

vaers.symptoms

where

symptom3 is not null

union all

select 

vaers_id,

symptom4 as symptom,

symptomversion4 as symptomversion

from 

vaers.symptoms

where

symptom4 is not null

union all

select 

vaers_id,

symptom5 as symptom,

symptomversion5 as symptomversion

from 

vaers.symptoms

where

symptom5 is not null

);

create index ix_allsymptoms_vaers_id on vaers.allsymptoms using btree (vaers_id);

create index ix_allsymptoms_symptom on vaers.allsymptoms using btree (symptom);

drop table vaers.vax ;

create table vaers.vax 

(

id serial,

VAERS_ID varchar,

VAX_TYPE varchar,

VAX_MANU varchar,

VAX_LOT varchar,

VAX_DOSE_SERIES varchar,

VAX_ROUTE varchar,

VAX_SITE varchar,

VAX_NAME varchar

)

WITH (

  OIDS=FALSE

);

--msdos postgres 9.3

--cat 2021VAERSSYMPTOMS.csv|psql -h localhost -d postgres -a -c "set client_encoding=latin1; copy vaers.symptoms (VAERS_ID, SYMPTOM1, SYMPTOMVERSION1, SYMPTOM2, SYMPTOMVERSION2, SYMPTOM3, SYMPTOMVERSION3, SYMPTOM4, SYMPTOMVERSION4, SYMPTOM5, SYMPTOMVERSION5) from stdin delimiter ',' CSV HEADER"

--cat 2021VAERSVAX.csv|psql -h localhost -d postgres -a -c "copy vaers.vax (VAERS_ID, VAX_TYPE, VAX_MANU, VAX_LOT, VAX_DOSE_SERIES, VAX_ROUTE, VAX_SITE, VAX_NAME) from stdin delimiter ',' CSV HEADER"

create index ix_vax_vaers_id on vaers.vax using btree (vaers_id);

drop table if exists vaers.data;

create table vaers.data

(

id serial,

VAERS_ID varchar,

RECVDATE varchar,

STATE varchar,

AGE_YRS varchar,

CAGE_YR varchar,

CAGE_MO varchar,

SEX varchar,

RPT_DATE varchar,

SYMPTOM_TEXT varchar,

DIED varchar,

DATEDIED varchar,

L_THREAT varchar,

ER_VISIT varchar,

HOSPITAL varchar,

HOSPDAYS varchar,

X_STAY varchar,

DISABLE varchar,

RECOVD varchar,

VAX_DATE varchar,

ONSET_DATE varchar,

NUMDAYS varchar,

LAB_DATA varchar,

V_ADMINBY varchar,

V_FUNDBY varchar,

OTHER_MEDS varchar,

CUR_ILL varchar,

HISTORY varchar,

PRIOR_VAX varchar,

SPLTTYPE varchar,

FORM_VERS varchar,

TODAYS_DATE varchar,

BIRTH_DEFECT varchar,

OFC_VISIT varchar,

ER_ED_VISIT varchar,

ALLERGIES varchar

)

WITH (

  OIDS=FALSE

);

--msdos postgres 9.3

--cat 2021VAERSDATA.csv|psql -h localhost -d postgres -a -c "set client_encoding=latin1; copy vaers.data (VAERS_ID,RECVDATE,STATE,AGE_YRS,CAGE_YR,CAGE_MO,SEX,RPT_DATE,SYMPTOM_TEXT,DIED,DATEDIED,L_THREAT,ER_VISIT,HOSPITAL,HOSPDAYS,X_STAY,DISABLE,RECOVD,VAX_DATE,ONSET_DATE,NUMDAYS,LAB_DATA,V_ADMINBY,V_FUNDBY,OTHER_MEDS,CUR_ILL,HISTORY,PRIOR_VAX,SPLTTYPE,FORM_VERS,TODAYS_DATE,BIRTH_DEFECT,OFC_VISIT,ER_ED_VISIT,ALLERGIES) from stdin delimiter ',' CSV HEADER"

create index ix_data_vaers_id on vaers.data using btree (vaers_id);

*/

select 

vv.VAX_MANU as manufaturer,

vv.VAX_NAME as vax_name,

VAX_TYPE,

RECVDATE,

count(distinct vd.vaers_id) as num_records

from 

vaers.data vd

left join vaers.allsymptoms vs on vs.vaers_id = vd.vaers_id

left join vaers.vax vv on vv.vaers_id = vd.vaers_id

where 

vs.symptom = 'Myocard%' 

--and not vd.died = 'Y'

group by

vv.VAX_MANU,

vv.VAX_NAME,

VAX_TYPE,

RECVDATE

;

-- example:

WITH D as

(

select 

vd.recvdate,

vd.state,

vd.age_yrs,

vd.sex,

vd.recovd,

vd.died,

vd.l_threat,

vd.hospital,

vd.disable,

vd.ofc_visit,

vs.symptom,

vv.vax_manu,

vv.vax_type,

vd.vaers_id

from 

vaers.data vd

left join vaers.allsymptoms vs on vs.vaers_id = vd.vaers_id

left join vaers.vax vv on vv.vaers_id = vd.vaers_id

where

vs.symptom_text ilike '%myocardi%'

)

select 

*

from D

limit 10

Analysis of ICSR reports at ema.europa.eu

Technical documentation to the article titled:

"The Costs of Covid-19 Vaccinations – Should we Rethink the Policy?"

This post provides documention for the analysis process that was performed with the abovementioned article (this link), as well as some additional visualisations produced from the data downloaded from EMA and ECDC.

Vaccination Volume Data from ECDC

The data for COVID-19 vaccination volumes can be found here:

https://www.ecdc.europa.eu/en/publications-data/data-covid-19-vaccination-eu-eea   

Individual Case Safety Reports from EMA

1. To download all ICSR reports, follow the steps below.

Open http://www.adrreports.eu/en/search_subst.html, navigate to 'C' and search for COVID-19.

 

To download ICSR reports for ALL forms of medication, one would need to visis the 4,000+ entries listed. As a workaround, I have a shortcut described below.

Since EMA does not allow the public to download all ICSR reports for all forms of medication in one go, I came up with a work around, by manipulating the url for entering their Oracle back end. By simply not specifying the identifier for a parrticular substance, all ICSR reports on all forms of medication get shown.

Shortcut to all Substances (incl. COVID19-vaccines)

Generate and download the ICSR Line listings for COVID, Measles and Influenza vaccines as well as the shortcut for all forms of medication, and repeat steps 2, 3 and 4 explained below, for each of the vaccines:

2. Export the ICSR reports to TAB-delimited text files as follows:

Navigate to the tab labelled 'Line Listing'.

For Geographic Region, select 'European Economic Area'.

Next, click on 'Run Line Listing Report'. This will open a new window and present you with the ICSR reports in tabular format. This may take a while.

Navigate all the way to the bottom and start the export as shown in the image below:

The export will be saved to the default Downloads folder of your web-browser.

3. Convert and rename all exported files to UTF-8 encoding (e.g. using Notepad++ for Windows).

In the instructions below, I used a naming convention as follows: MMMDD_export_[substance].csv

4. Load the exported file into PostgreSQL

Create a schema and table in PostgreSQL (I use an old version 9.1 on an old Windows Server 2008)

CREATE SCHEMA ema;
CREATE TABLE ema.sta_icsr
(
  source varchar,
  elocnr character varying,
  reporttype character varying,
  evgatewayrecdate character varying,
  primarysourcequalification character varying,
  primarysourcecountryforregulatorypurposes character varying,
  literaturereference character varying,
  patientagegroup character varying,
  patientagegroupperreporter character varying,
  parentchildreport character varying,
  patientsex character varying,
  reactionlist character varying,
  suspectdruglist character varying,
  concomitant character varying,
  icsrform character varying
)
WITH (
  OIDS=FALSE);

Next, load all ICSR exports into the table. I used the following DOS command:

for /F %f in ('dir/b APR13_*.csv') do tail -n +2 %f|sed -e s#^^#%f\t#|sed -e s#\xED\xAF\x80#t#g -e s#\xED\xB6\xA9#t#g -e s#\xed\xb6\x9f#i#g -e s#\\#\\\\#g|psql -h localhost -U postgres -a -c "copy ema.sta_icsr from stdin"

Description of the DOS command: For each export file (%f), skip header, add a column identifying the filename, replace some unreadable characters, prepend backslashes with a backslash and tell psql to execute the copy command.

5. De-duplication of records

To de-duplicate, we need a table that holds only unique entries. Also, we need to give priority / precedence to specific substances, before we load the rest (all substances thru that manipulated url).

create table ema.dwh_geneloc (
id serial,
source varchar,
elocnr varchar
)
without oids;

insert into ema.dwh_geneloc (source, elocnr)
select
source, elocnr 
from 
ema.sta_icsr
where 
not (elocnr) in (select elocnr from ema.dwh_geneloc group by elocnr)
and source like '%pfizer%'
;
insert into ema.dwh_geneloc (source, elocnr)
select
source, elocnr 
from 
ema.sta_icsr
where 
not (elocnr) in (select elocnr from ema.dwh_geneloc group by elocnr)
and source like '%astrazeneca%'
;
insert into ema.dwh_geneloc (source, elocnr)
select
source, elocnr 
from 
ema.sta_icsr
where 
not (elocnr) in (select elocnr from ema.dwh_geneloc group by elocnr)
and source like '%moderna%'
;
insert into ema.dwh_geneloc (source, elocnr)
select
source, elocnr 
from 
ema.sta_icsr
where 
not (elocnr) in (select elocnr from ema.dwh_geneloc group by elocnr)
and source like '%janssen%'
;
insert into ema.dwh_geneloc (source, elocnr)
select
source, elocnr 
from 
ema.sta_icsr
where 
not (elocnr) in (select elocnr from ema.dwh_geneloc group by elocnr)
and source like '%MMR%'
;
insert into ema.dwh_geneloc (source, elocnr)
select
source, elocnr 
from 
ema.sta_icsr
where 
not (elocnr) in (select elocnr from ema.dwh_geneloc group by elocnr)
and source like '%Influenza-split-virion-inactivated%'
;
insert into ema.dwh_geneloc (source, elocnr)
select
source, elocnr 
from 
ema.sta_icsr
where 
not (elocnr) in (select elocnr from ema.dwh_geneloc group by elocnr)
and source like '%influenza-live-nasal%'
;
insert into ema.dwh_geneloc (source, elocnr)
select
source, elocnr 
from 
ema.sta_icsr
where 
not (elocnr) in (select elocnr from ema.dwh_geneloc group by elocnr)
and source like '%all_all%'
;

6. Create some indexes to speed up query performance

create index ix_staicsr_source on ema.sta_icsr using btree (source);
create index ix_staicsr_elocnr on ema.sta_icsr using btree (elocnr);
create index ix_geneloc_source on ema.dwh_geneloc using btree (source);
create index ix_geneloc_elocnr on ema.dwh_geneloc using btree (elocnr);

7. Run query and export results to a text file

select

i.source,

split_part(split_part(i.source, 'apr13_', 2), '_', 1) as product,

i.elocnr,

date(to_timestamp(EVGwayRecDate, 'yyyy-mm-dd')) as recvd_date,

patientagegroup,

patientsex,

case 

when primarysourcequalification like 'Non Health%' then false

else true

end as hcp_reported,

replace(split_part(unnest(string_to_array(reactionlist, ',<BR><BR>')), E'\x20\(', 1), '"', '') as Adr_Text,

split_part(replace(split_part(unnest(string_to_array(reactionlist, ',<BR><BR>')), E'\x20\(', 2), '"', ''), ' - ', 2) as Adr_Outcome

from

ema.dwh_geneloc e

join ema.sta_icsr i on e.source = i.source and e.elocnr = i.elocnr

Save the query output to disk, so that you can pick ip up with a BI-tool, such as Tableau.

8. To select only Fatal reactions, this query will do the job:

WITH all_icsr AS

(

select

i.source,

split_part(split_part(i.source, 'apr13_', 2), '_', 1) as product,

i.elocnr,

date(to_timestamp(EVGwayRecDate, 'yyyy-mm-dd')) as recvd_date,

patientagegroup,

patientsex,

case 

when primarysourcequalification like 'Non Health%' then false

else true

end as hcp_reported,

replace(split_part(unnest(string_to_array(reactionlist, ',<BR><BR>')), E'\x20\(', 1), '"', '') as Adr_Text,

split_part(replace(split_part(unnest(string_to_array(reactionlist, ',<BR><BR>')), E'\x20\(', 2), '"', ''), ' - ', 2) as Adr_Outcome

from

ema.dwh_geneloc e

join ema.sta_icsr i on e.source = i.source and e.elocnr = i.elocnr

)

select

    *

from

    all_icsr

where

    adr_outcome ilike '%fatal%'

9. Beware of difference between ICSR and ADR

Within EMA, an ICSR report relates to a patient / person.

An ICSR report can record multiple reactions and corresponding outcomes.

In counting the number of deaths per 100K vaccines, you should therefore not count number of reactions with fatal outcome, as this could result in multiple fatal reactions per patient.

In the article, we have used the distinct count of unique ICSR reports. 

The query below illustrates the difference between the two measures:

with all_reports as 

(

select

i.elocnr,

split_part(split_part(i.source, 'apr13_', 2), '_', 1) as product,

split_part(replace(split_part(unnest(string_to_array(reactionlist, ',<BR><BR>')), E'\x20\(', 2), '"', ''), ' - ', 2) as adr_outcome

from

ema.dwh_geneloc e

join ema.sta_icsr i on e.source = i.source and e.elocnr = i.elocnr

)

select 

product,

count(*) as num_adr,

count(distinct elocnr) as num_icsr

from 

all_reports

where 

not product = 'all'

adr_outcome ilike '%fatal%'

group by

product