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TNF inhibitor drugs (for atopic dermatitis) and COVID-19

Researchers
#1

Hi all, I am Akari,
I would love to have a study using OHDSI tools about the relationships between TNF inhibitor drugs used by atopic dermatitis patients and the symptoms of COVID-19.

However, because it is for my EE, (extended essay in IB curriculum where I need to research, analyze, and write the report on my own.) The purpose of EE is to see whether I can write a research paper, not about the content.

Are there any ways for me to get the data and conduct an analysis by myself?
Thanks again.

@krfeeney @Daniel_Prieto

Regards,
Akari

PS
How do I get my full access (to define the cohort) to ATLAS?

#2

@akajpn

To define cohorts, make sure you are at http://www.ohdsi.org/web/atlas/#/cohortdefinitions

The other Atlas (https://atlas.ohdsi.org/#/cohortdefinitions) does not have definition permissions enabled.

Best,

Jon

2 Likes
#3

Hi @akajpn! Welcome!!

We have a lot of existing research in COVID. It’s good to take advantage of what’s already been done. You can see our cohorts from our characterization study: Covid19CharacterizationCharybdis/CharybdisPhenotypeLibrary.csv at master · ohdsi-studies/Covid19CharacterizationCharybdis · GitHub

You can also check out @Gowtham_Rao’s OHDSI US Symposium presentation about the Phenotype Library. There maybe some atopic dermatitis concept sets that you could reuse.

So the way it works is this:

  1. You can take advantage of the existing results set that’s on data.ohdsi.org. Check out Charybdis and Scylla Characterization.
  2. You can join the Charybdis 2.0 work and add your question into our big protocol. We are kicking this off in the new year. I believe someone else has brought up atopic dermatitis but I am blanking on the name. @Daniel_Prieto or @tduarte might recall. :wink:

Do you have access to the OHDSI Teams environment? If not, @ekatzman can help you out!

Now many folks are taking a couple of weeks off to recharge around the holidays, myself included. We would be happy to connect with you in the new year! What is your timeline for your class assignment?

BTW fun fact: @jon_duke speaks awesome Japanese and he knows ATLAS. :smile:

1 Like
#4

Thanks, @krfeeney, and @jon_duke!

Actually, I do have a very tight schedule for my report.
My goal is to finish defining cohort by the first week of January. (I’ve got nothing else to do except this report).

Have a nice holiday! :smile:

Best regards,
Akari

#5

Hi @krfeeney,

How were your holidays?
I’ve been working on my research, and I decided to have characterization analysis related to corticosteroids use in AD patients and COVID19.

I couldn’t identify the cohorts for COVID19, used in Charybdis study. Where can I find it?

#6

Hi @akajpn!

Too short. :wink: How about you? :slight_smile:

All of the cohorts in Charybdis are available in this CSV list. We have ATLAS and JSONs links in here: Covid19CharacterizationCharybdis/CharybdisPhenotypeLibrary.csv at master · ohdsi-studies/Covid19CharacterizationCharybdis · GitHub

Charybdis thinks like this. We cut a count of the people in a Target cohort (e.g. the flavors of COVID-19 and the Flu). We then stratify the Target cohort by a number of custom stratum (all labeled as Stratum in the list). We then create a count of the Features that are within the Target-Stratum combination.

The cohort IDs you might be interested in are Cohort 132, 134 and 136. These are (1) COVID-19 diagnosed or tested positive with 365 days of prior history before their index, (2) hospitalized with COVID-19 diagnosed or tested positive with 365 days of prior history before their index and (3) hospitalized, receiving intensive services (aka proxy for ICU – it’s hard to find this reliably so we used procedure codes indicative of intensive care units) with COVID-19 diagnosed or tested positive with 365 days of prior history before their index.

There’s currently no Stratum for Atopic Dermatitis individually. So in the available results you could look at the CONDITION_ERA (and search ‘atopic dermatitis’ it will show up as a string and what that represents is the way atopic dermatitis is represented in the SNOMED hierarchy) and see the counts of people who are in that Target cohort with atopic dermatitis.

Now, in Charybdis we didn’t actually pull custom definitions for drugs. We just have DRUG_ERAs (derived from the drug_exposure table) and those are by the ingredient level. But there’s another study you could use. You can look at Scylla Characterization shiny app to see information characterizing these: https://data.ohdsi.org/ScyllaCharacterization/

The challenge you’ll see is that we don’t have the intersection of what you really want which is COVID-AD-drug exposure. I’m sorry to say that’s a gap at the moment. But maybe there’s a view here that’s still usable.

1 Like
#7

Hi, sorry for the late reply.
Holidays are always short :wink:

I could see that there are no cross-sectioned data with condition occurrence and drug exposure.
Is it okay to ask to run the data once I make a package in ATLAS with a research protocol??

Thank you for your support :blush:
Akari

1 Like
#8

Hi Akari!
Ahhh sorry missed this: Yes! Write up a protocol and I can help you get this into code/get results. :slight_smile:

1 Like
AD Corticosteroids and COVID severity
#9

Hi @krfeeney,

I worked on my study protocol :smile: I am almost there, but I would like to hear the next general step (or where I can find the procedures).
It was more difficult than I thought, but I had so much fun!!!
I would like to run characterization analysis to see how many atopic dermatitis patients have taken corticosteroids, with in COVID features.

P.S.
I have been getting 513 error for my ATLAS, so was working on ATLAS.demo.
Is it fine?

Study Protocol (Characterization Study).pdf (134.9 KB)

#10

@krfeeney, (and other OHDSI members)

Hi, my submission day for the report is coming soon.
It will great to know what I should do now by this week.
Thank you.
Akari

#11

Hi @akajpn!
Thanks for the poke. I was swamped last week and lost track of my to do list. I will try to run this on our data tomorrow. Will send you what I get!
Best,
Kristin

1 Like
#12

Thank you!

#13

Hi @krfeeney
I think I forgot to add link for ATLAS.
http://atlas-demo.ohdsi.org/#/cc/characterizations/424
Please let me know if there is any problem.
Regards,
Akari

1 Like
t