search

CRI-iAtlas / iatlas-app

R Shiny app for CRI iAtlas, an interactive web portal for exploring immuno-oncology data. (iAtlas portal 2022 and beyond)
Other
12 stars 3 forks source link

Inconsistencies in Responder/Progression/Clinical_Benefit annotations #214

Closed jaeddy closed 1 year ago

jaeddy commented 2 years ago

Opening this issue on behalf of Aik Choon Tan at the Moffitt Cancer Center:

Thanks for developing the useful CRI iAtlas web portal, and also recently adding the new data sets on immunotherapy in the portal.

However, recently, when we tried to download the data iatlas-ici-features.tsv from Synapse, we noticed that some data sets have the Responder/Progression/Clinical_Benefit labels flipped. For example, if you look at the Riaz data set, Riaz_Nivolumab_2017-p001-ar-8813 has a response “Progressive Disease”, however the Responder column is flagged as “TRUE”, and the “Progression” column is also flagged as “TRUE”, and the Clinical_Benefit is flagged as “FALSE”. Similarly, if you look at the Riaz_Nivolumab_2017-p001-ar-8877, which is a “Partial Response”, the Responder column is flagged as “FALSE” and the Progression is also flagged as “FALSE”. There are some samples in VanAllen, as well as the IMvigro and IMmotion.

image

In addition, in the iAtlas page, the definition of “Responder” is PR or CR, and “Non-Responders” are SD or PD. But if you look at the Riaz_Nivolumab_2017-p001-ar-8815, the Clinical_Benefit column is flagged as “TRUE”.

image

I think this a great resource to the community, and it will be helpful to provide the correct labels for researchers to download and do their analyses.

Thanks again for your great product! Happy to discuss more if needed.

andrewelamb commented 2 years ago

@heimannch This is the fix you made to the database last week correct?

@jaeddy If so, once the database rebuilds this will be fixed.

heimannch commented 2 years ago

Yes! And I also already updated the iatlas-ici-features.tsv file on Synapse.

ychae commented 2 years ago

Waiting on the deployment fix from Xa and Jon

milen-sage commented 2 years ago

What is the status on this? And what's the AC?

ychae commented 2 years ago

The bug has been fixed but we're stuck on deploying the fix until the database build issue has been resolved (Xa is working on this with Jon from GenUI)

ychae commented 2 years ago

AC: Update the iatlas-ici-features.tsv to reflect the correct responder information (some labels are flipped) and deploy the fix to the live production app.

heimannch commented 2 years ago

FYI: iatlas-ici-features.tsv is already updated with the correct version.

ychae commented 2 years ago

Blocker: Database build issue has not been resolved. I've reached out to Sage IT and GenUI as couple times about this (including today) but haven't heard anything. @jaeddy would you be able to help us escalate this?

moving this to our backlog until the DB build issue is resolved.