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Adding new vocabularies

CDM Builders
#1

In the Netherlands we use ICPC1 for conditions and for drugs we use z-index.

My questions are about the procedure to add this to the OHDSI vocabularies.

  1. If it turns out that there are license requirements, how does this work? I see the other vocabs with licenses which require probable @Christian_Reich and this team to approve the request before sending the vocab. Does this mean that the Athena maintainer (Christian?) must have a license as well?

  2. ICPC1 is pretty stable over the years, but if there are changes who will then update the mapping? in other words if this is added to the official vocabs will it then be maintained by the vocab team?

  3. Will there be a quality control step done by the vocab team on the mappings before it is added to Athena etc?

  4. We are also reviewing our drug mappings (z-index to RxNorm). We know z-index has a big license fee and we will most probably not be able to share is. However, a mapping from a z-index to RxNorm concept is not revealing the full z-index with all its details, maybe this is allowed? any experience with this in de vocab team?

  5. If we are not able to share vocabs we could of course just add them locally as concepts but then we need to make sure these conceptIDs will not be used later for other purposes. We could (i think) share these mappings with others in the Netherlands that have z-index licenses. Any ideas about this? This is not a preferred option of course.

Thanks

#2

@Rijnbeek:

You never got an answer. Sorry about that. Please do ping us if there is radio-silence. It’s not that you are not loved. :smiley: It’s just the normal craziness of things.

  1. The “vocabulary maintainer” (really the Odysseus team, I am just providing some direction) does all the work, but what we need is a re-distribution license for Columbia as the Coordinating Center. That’s not a normal user license. And we need it for free. We should talk to the ICPC1 and z-index people and ask them. Usually, they first are very skeptical, but when we explain what we are doing they calm down quickly.

  2. The Odysseus team who runs Athena. They already have drug vocabularies from Canada, England, Germany, France, Japan and Australia. So, join the club.

  3. Yes, definitely. It’s all in Github. However, we are working on a new automated system called Pallas. There is no Github for that quite yet.

  4. The way it works is like with all the commercial vocabularies: We get that re-distribution licence and use it to create the mapping. If somebody has data in z-index and wants to download the mapping from Athena, that person will have to prove that the organization has the commercial license. Works the same way with FDB, Medi-Span, MedDRA, etc. Without it, Athena is going to refuse adding that vocabulary into the download zip file. It’s pretty clean. BTW: Mapping to RxNorm is no longer what we are doing. We are now creating RxNorm Extension for all those products that arte not sold in the US. They get added to the overall system using a semi-automated mechanism.

  5. Don’t do it. If the z-index people are afraid to put it onto Athena, we should still run it through the RxNorm Extension job. Otherwise, maintenance is going to be hell. And yes, if some Dutch guy needs it, we’d provide it outside Athena. But let’s try to avoid it, each such exception is a tremendous burden on the team and myself.

Let’s talk about how to move this forward.

#3

Hi Christian thanks for the reply it was worth the waiting haha.

By now we have already mapped most of ICPC1 and a lot of the z-index for our ETL and are sharing this with another Dutch database that is currently mapping, but there is still a lot to optimise i think and life would be much easier for us if it was in the vocab so we can search on it.

I can ask around for the contact persons internally for the two vocabs so they can be contacted to discuss the possibilities.

You will hear from me soon.

Peter

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