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Patient-level data for covid-19 from diverse sources, how can we standardize those?

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#1

I found four patient-level datasets from Korea, Singapore, Hongkong, and US.
Can we standardize these datasets?

I posted this issue to the github, too.

4 Likes
#2

Hi @SCYou,

I am from Singapore and would be interested to participate in this effort.

Currently we have standardized our questionnaire and put it into cdm.observation table.

Is that what you are asking?

1 Like
#3

@SELVA_MUTHU_KUMARAN , do you mean results of questionnaires for suspected covid-19 patients in Singapore? Then, yes, it would be what I’ve been looking for!

#4

Sorry, no. I didn’t mean that. What I meant was we usually standardize our other survey questionnaires from hospital and put it into observation table.

btw @SCYou - May I know whether you want to just convert the questionnaires (questions) which are hand out to the covid-19 patients?

Or if you wish to have access to their (covid-19 patients) responses, then I guess it might take a bit of time

I was told that it is sensitive and not open as of now

#5

looks great! The hongkong database needs a bit patient information collection and formatting. I can offer some time to convert if we fix the strings that need to be collected. Let me know where I can join.

1 Like
#6

Count me in as well. Happy to be involved

1 Like
#7

I’m happy to get involved

#8

I’m going to spend some time today to download and convert into structured fromat (e.g. csv or json) from html
this source https://wars.vote4.hk/en/cases/

#9

Hongkong data is already available as spreadsheet: https://docs.google.com/spreadsheets/d/e/2PACX-1vSr2xYotDgnAq6bqm5Nkjq9voHBKzKNWH2zvTRx5LU0jnpccWykvEF8iB_0g7Tzo2pwzkTuM3ETlr_h/pub?gid=0&range=A2:ZZ

2 Likes
#10

Kudos! This is great information.

#11

On date of confirmed diagnosis, we do:

CONDITION_OCCURRENCE:

condition_cid=<covid19> (from snomed 840539006 , see https://www.wikidata.org/wiki/Q84263196)

(Jan 2020 snomed seems not to be in Athena web version) No results when doing

http://athena.ohdsi.org/search-terms/terms?query=840539006&page=1

Symptom onset

would go to OBSERVATION

#12


There are cases from the Hong Kong source
I created GitHub PR too.

2 Likes
#13

These datasets are very useful for research, thanks for sharing! I will try to hunt down if there is any open data in The Netherlands from RIVM or NIVEL.

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