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Adding new vocabularies before they are mapped to standar concepts

(Javier Gracia-Tabuenca) #1


In short :
Could we submit our local vocabularies to be included to OMOP, and later when ready we the send the mappings to the standar conceps ?

In long:
We have our EMR data and our “rule/language system” to extract cohorts from it, but the code doing this seems buggy.
We are converting the data to the CDM and the rules to the atlas’s cohort definition .json format.

To make this conversion as compatible as possible the cohort definition searches by “source concept id”.

However, we use many national vocabularies that are not in OMOP, and therefore the source concept ID does not exists.

We would like to sent the national vocabularies now so that the CDM is able to solve our current problem.

(Oleg Zhuk) #2


Tagging some people, who can help you!
@Christian_Reich @mik

(Christian Reich) #3


That’s how it works, you got it. Let us know what vocabularies you have, where you get them from if they have to be refreshed from time to time, and let’s help you with the mapping. At least with advice.

(Selva) #4

@Christian_Reich - We have few cognitive assessment questionnaires used at our end like RBANS, GDS, etc. Currently, we have created local concepts. So can these be made as standard concepts as well?

If it is not found to be useful for the wider community and only useful for Singapore, would you still consider it?

However, I feel those assessments are conducted across the globe anyway.

(Michael Kallfelz) #5

@Javier There is actually a bit of a process for this in place!
I gave a quick recap of it in one of the last community calls:

As you can see in the diagram of the slide deck, there is a new demand workflow. After you have identified a vocabulary that you deem worthy to become a standardized one, collect as much information about it, as you can and bring the case forward to the CDM workgroup. This is followed by a process of assessment and prioritization to assign the limited resources meaningfully.

And @Christian_Reich is a good ally to have! He can be very persuasive… We are thrilled to hear about your local / national vocabularies, the more in use in your region and the more standardized already, the better (and the more interesting). And quite often, synergy can be found, because we hear things and can connect you. We currently are looking at a number of European vocabularies, to some degree triggered by the EHDEN CoViD-19 rapid call.
Looking forward to hearing from you!

And @SELVA_MUTHU_KUMARAN, this sounds like you should get in touch with the Psychiatry Working Group. They might come up with a couple of best practice approaches here.

(Javier Gracia-Tabuenca) #6

Thanks a lot, we’ll follow this guide lines