OHDSI Home | Forums | Wiki | Github

Steering committee: Proposal to Standardize Network Studies


(Martijn Schuemie) #1

Continuing the private conversation that came out of the Steering Committee meeting on the forums:

@Christian_Reich, @gregk, I would say:

  1. Creating a clinicaltrials.gov, but for OHDS studies
  2. Disseminating study code

Let’s not have the “can’t have R packages” discussion again. See here and here.

ARACHNE: I * think * ARACHNE might be useful for OHDSI, but I have yet to see it in action. If we are serious about implementing ARACHNE in the OHDSI network, I recommend:

  1. Creating documentation on how to install ARACHNE (or is it already somewhere? Google can’t find it)
  2. Creating documentation on how to use ARARCHNE
  3. Use ARACHNE in some pilot OHDSI network studies
  4. Learn from these experiences to find out real-world requirements for ARACHNE, and make it really good

As Kristin mentioned, I would mostly be interested in getting some minimum meta-data in place to help make some sense of what is in which repo. I moved one of my study repos into ohdsi-studies, and have added some example minimum meta-data elements to the README.


(Christian Reich) #2

Well, but then we need to actually conclude and come up with a solution that takes care of the various issues. I understand not all studies can be pre-scanned, but you have to understand that the opposite is not feasible either: All studies are R packages with more or less unknown (to the security people) content. We need to have the standard studies pre-canned and JSON-configured, and we need a way to do something that breaks that. In that case, the institution can implement the former, and have some tight governance oversight bureaucracy for the latter. Makes sense?

I don’t understand the proposal here, mostly because of unfamiliarity with the technology.

Agreed.


(Gregory Klebanov) #3

yes, I agree - we did exchange a lot of ideas and opinions but I yet to see us coming up with an aligned and agreed approach / solution

But I also do think that @schuemie is right - “No R code” is just as extreme as “Everything should be in JSON and agreed upon”. There will be times when we need to be flexible and be able to exchange the code. However, I do think that we should follow 80/20 approach where 80% should be designed in ATLAS and have a standard definitions and code output.

Yes, agreed on all. The user manual and installation guide are [here] (https://github.com/OHDSI/ArachneUI/tree/develop/manual) - at least for now. I actually debated where these docs should live, will eventually move some content to WIKI, or at least have some “Start here” document in WIKI

I would love to see us (OHDSI) using ARACHNE in ager on some OHDSI study (ies) and then learn from that experience. Any ideas what study - or multiple studies - we could use?


(Martijn Schuemie) #4

@Christian_Reich: ok, sure. I’ve added your wish as item 58 on the Neverending List of Fun Things To Do. Perhaps you can find a skilled R programmer who can do this? I’d be happy to advise.

@gregk: thanks for putting the documentation online. Focusing just on the installation instructions, I have some further recommendations that you can take or leave:

  1. As per @Rijnbeek’s comments, I would add some introduction, and just some context for people (like me) that aren’t completely familiar with the ins and outs of ARACHNE. For example: what is an ARACHNE Portal? An ARACHNE Datanode?
  2. I recommend having an HTML version as well. I would not recommend the Wiki, since I think we’re slowly moving away from that as a community. One example to consider is the Methods Library documentation.
  3. Currently the documentation assumes some Linux variant. You’d have many more people willing to try it (like me) if you could also do it in Windows. (On the database side you’re pushing for OHDSI to support every database platform imaginable, so you should feel the same way about deployment platforms :wink: )

I know writing documentation isn’t the most fun, but it is an essential part of any software product.


(Christian Reich) #5

Wait. That skilled R programmer exists. He already did it. We were able to execute R code by sharing JSON configuration files between ATLAS instances, and an the execution engine could take it and create results. That was a year and a half ago. Since then, somebody broke this model. Can’t remember who. :slight_smile:


t