Can CSVs containing information on events only be for one date?

[boverdui]

Hello,

Do I correctly understand that a CSV with event information to be used in White Rabbit can only contain information from one date? In other words, if I have event information for a full year, does this mean this should be divided over 365 CSV files?

With kind regards,
Bert Overduin (Aridhia Informatics Ltd)

[DrUrwin]

Hello @boverdui

If you could provide a little bit more information around this, it would help me understand your question better. Do you mean:
(a) one column for event dates containing multiple rows of dates?
or
(b) multiple columns for multiple event dates, each containing multiple rows of dates?

Please let me know, many thanks,

    Esmond

[boverdui]

Hello Esmond,

It's this paragraph in the documentation (https://carrot.ac.uk/standards) that isn't very clear to me, especially the passages I highlighted in bold:

One or more CSV files that contain event data, such as questionnaire responses or clinical events/measurements. As a minimum each CSV file must have a column that contains the anonymised ID for the individual (matching an entry in the CSV file above), the date of a particular event (one per file) and one or more columns that capture the data relevant to that date. You can have as many CSV files as needed, but each CSV file must only contain information effective on the specified event date.

With kind regards,
Bert

[DrUrwin]

Hi Bert,

Good question, thanks. In effect it means each CSV must have 1x ID column and 1x Date Event column (to map to), as per the following below:

ID Column || Date Event || Data Item 1 || Data Item 2 || ........ || Data Item 'n'

If you have multiple important date events that you want to map to in one table then this will not work within Carrot. You will need to segregate these and split them into separate CSVs/table, for example:

If we have a CSV/table with 3 date events that you want to map to as follows:

• ID Column || Date Event 'X' || Date Event 'Y' || Date Event 'Z' || Data Item 1 || Data Item 2 || ........ || Data Item 'n'

For Carrot, the above CSV/table will need to be broken into the following 3 CSVs/tables as follows:

• ID Column || Date Event 'X' || Data Item 1 || Data Item 2 || ........ || Data Item 'n'

• ID Column || Date Event 'Y' || Data Item 1 || Data Item 2 || ........ || Data Item 'n'

• ID Column || Date Event 'Z' || Data Item 1 || Data Item 2 || ........ || Data Item 'n'

Thus, for Carrot, each CSV / table needs:

• 1x ID column to map to
• 1x Date Event column to map to

I hope this helps

[boverdui]

Hello Esmond,

I'm sorry, I still don't get it. Does that mean that in one CSV file the value of Date Event is the same for each row?

With kind regards,
Bert

[boverdui]

Hello Esmond,

I am still not 100% sure if I understand completely what you are saying. For example, would the attached file (which contains only fake data), be valid or is it not in the right format?

Cheers,
Bert

lab_test.csv

[DrUrwin]

Hi Bert,

The fake data in the CSV looks fine to me. That would need to be fed into the OHDSI WhiteRabbit tool to create a Scan Report. The Scan Report would then be uploaded to Carrot to map to OMOP.

Regards,

  Esmond

[DrUrwin]

Hi Bert,

If you'd like a 1-2-1 meeting in Teams please do ask

Esmond

[boverdui]

Hi Esmond,

Thanks!

It was the paragraph on the https://carrot.ac.uk/standards page that really confused me:

(1) "One or more CSV files that contain event data, such as questionnaire responses or clinical events/measurements. As a minimum each CSV file must have a column that contains the anonymised ID for the individual (matching an entry in the CSV file above), the date of a particular event (one per file) and one or more columns that capture the data relevant to that date."

I now assume that "one per file" means to say "one event_date column per file". I initially read this as "one date per file". I'd suggest to rephrase this more clearly.

(2) "You can have as many CSV files as needed, but each CSV file must only contain information effective on the specified event date."

I'm still not sure what is meant here (nor does my colleague who I showed this to). I'd suggest to either rephrase this or omit it completely.

Cheers,
Bert

[DrUrwin]

Hi Bert,

Your points are valid and we're looking to re-write this section very soon to make it clearer and easier to use, thanks.

Esmond