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COVID-19: Data Sharing/BR

(Rita Rb-Silva) #1


From rda-covid19-community:

"Good day!

Are the kind colleagues aware that FAPESP (BR) has just launched a mega-repository of COVID-19 data, asking for FAST FEEDBACK in order to make improvements?
( https://repositoriodatasharingfapesp.uspdigital.usp.br/ )

  • Feedback is wanted from COVID researchers, as well as data/data science experts.
  • The initial set of 75,000 patients and 1.5 million registrations will be made available “open & free” from the 1st of July. Thereafter, periodic additions will occur and, starting in October (prove.), images (tomographies and analogues and their reports) will also be added.
  • The research group shows high interest in open data.
  • The pilot set presents 300 patients.

The request for feedback runs until 24-June to the email covid19datasharing @ fapesp.br

Wide dissemination is well appreciated!
Many thanks for the kind attention!"

(Patrick Ryan) #2

Thank you @rita.rbsilva, this sounds like it will be a tremendously valuable resource and I wasnt aware of it. I was a bit confused from the link you provided, can I download the pilot data now (if yes, apologies I couldnt find it). This seems like it would be a great opportunity for the community to come together to rapidly develop an ETL to OMOP CDM, so that when the full dataset becomes available, we’d be ready to use these data, including running CHARYBDIS. Is there anyone in the community who’d like to lead that?

(Rita Rb-Silva) #3

@Patrick_Ryan, you can download the pilot data (available since june 17th) using the following links:

The data is split in different files according to the source, but I did not download any file yet. I only shared the post because it seemed something that could be of interest to the OHDSI community.

(Christian Reich) #4


This could be cool indeed. I took a look. Right now, there are three institutions sharing data, which consist of demographics and lab tests (covid and others). Do you expect longitudinal data to show up as well?

(Rita Rb-Silva) #5


From what I know, they included all the available lab results of the individuals submitted to a covid-19 test since november 2019. Some individuals may have repeated a lab analysis, but “real” longitudinal data (multiple evaluations of the same parameter(s) at specific time points) probably won’t be included.

Feedback is needed until june 24th. All sugestions should be sent to covid19datasharing@fapesp.br

Based on this feedback, a few additional features will be added by July 1st. From then on, new data will be periodically made available and the repository will be increased and updated - with the inclusion, among others, of image files, all of which open.

(Christian Reich) #6

Happy to write to them, but trying to avoid saying the obvious that they already stated. Here is the thing: The demographic and lab tables are fine. All we need. But is there a plan to add the clinical data? Like symptoms, diagnoses, procedures, drugs, visits? Without them, we can’t do much research. Anything I am missing?

(Rita Rb-Silva) #7

That’s true… I am not involved in the project at all, but I wrote to them to better understand their plan.