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SNDS Mapping


(Arnaud Ch31) #1

Hello everyone,

I am currently looking at various datasources in France, and especially the SNDS, which include the PMSI data. I was asking myself if any ETL to the CDM version 6.0 was already made giving the fact that I saw a publication on the database:

Empirical assessment of case-based methods for drug safety alert identification in the French National Healthcare System database (SNDS): Methodology of the ALCAPONE project

From what I understand on the process the team actually used small extracts to do their study, and then map these extracts to the CDM. In that view, did the team generated any ETL that I could reuse, either on their data extracts or maybe directly on the full SNDS.

Looking forward to hear from the community and maybe directly from the team that worked on this project, unfortunately I couldn’t find their pseudo in the forum. Can exchange here or over phone. In any case happy to connect.


(Christian Reich) #2

@Arnaud-CH31:

There were preliminary conversations to help the National Datahub (or whatever it is called in French) convert the entire SNDS to OMOP, and stop the business of doing that for extracts only. It’s silly anyway, because the strength of this approach is that you avoid endless duplication of labor and you can use the entire database for efficient and reproducible cohort definition and building strong probabilistic models.

Let’s bring them in.


(Arnaud Ch31) #3

Hello Christian,

Yes totally agree, plus the healthdataHub (that’s how it is called aha), has already tons of already formatted on CSV and JSON nomenclatures that can be used with OHDSI tools. They have already implemented all files required to initiate the mapping in their GitHub repository

   [https://gitlab.com/healthdatahub/schema-snds]

I have started to talk with them in order to see if I can get small sample like the SYNPUF, but not succeeded to obtain any answer yet. I am quite familiar with these datasets, and willing to help map it to the CDM, especially for the MCO - PMSI (Inpatient dataset).

Plus if they are actually trying to pull up a new structure to allow more access for healthcare actors through a centralised database of all the parts of the SNDS, it would make no sense not taking into consideration the CDM if they are reforging it.
As I am still quite young in understanding how the community proceed, what would you propose as next step to bring them in ?
Happy to drive this but I am not yet an expert on the CDM even though I already have some experience.


(Antoine Lamer) #4

Hi @Arnaud-CH31 ,

@Matthieu initiated vocabulary mapping from SNDS to OMOP, you can found some information here European coding vocabularies.


(Arnaud Ch31) #5

Hello @AntoineLamer,

Yes I have already seen this post, and indeed this is a start for mapping drug medication, and associated costs. Nonetheless nothing have been initiated on the procedure side (CCAM codes) from what I can understand.
Plus it seems that the HealthDataHub team is more around the mapping of drug codes to standard concepts using probably Usagi, if we can plug another workstream around the data mapping to CDM (knowing that nomenclatures will come along) we can maybe gain some time.
I would be more than happy to have a call with @Matthieu or you to better understand what the HealthData hub is mapping and avoid duplication of efforts like @Christian_Reich mentioned.

Looking forward hearing from you guys, let’s build this up together :wink:


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