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Complete list of all OMOP vocabularies and their versions

Vocabulary Users
#1

Dear all,

I am wondering about two things regarding vocabularies.

  1. Where do I find a complete list of al OMOP vocabularies. I see that there is a list of Vocabularies in Athena. But I also see list of vocabularies in this documentation, but I find that those lists are not 100% the same. My question is where do I find list of al OMOP vocabularies.

  2. Once I have a list of all OMOP vocabularies, I need to know which version is currently being used in CDM so that I can make sure that the vocabularies I have match OMOP version. I got info that versions are found in the VOCABULARY table, which is part of the download from Athena. I could download that table, but it was incomplete with the vocabularies that require license. How do I address that issue? And is there any other source besides from Athena that provides into on versions of the vocabularies.

Thank you in advance for help.
Kind regards,
Maja

#2

Hello Maja,
regarding the second of your questions: unfortunately, there is no way to see the licensed vocabularies when selecting from the VOCABULARY table if you do not have the license itself, and it is the right place to look for the versions. However, you can request such license through Athena and describe the reason you need to know the versions in the request.
Regarding the first question: can you please tell what vocabs you have found to differ between Athena and the Github list?

#3

Thank you Tatiana. That was very helpful.
Actually I found only two vocabularies missing in github.
The fist one Meas Type - OMOP Measurement Type - I did not find it in the Athena vocabulary list - but it was present in the VOCABULARY.csv after downloading all vocabs.
Second one - HGNC - Human Gene Nomenclature (European Bioinformatics Institute) - was listed in the Athena vocabulary list but was not present in neither the VOCABULARY.csv nor the github list.

#4

It seems like OMOP Measurement Type table goes as MedDRA on the GitHub page. The HGNC really seems to be missing from the list, but it can be downloaded separately from Athena. Thank you for bringing up these inconsistencies! Hope the difficulty has started resolving:)

#5

Dear Maja,
after further investigation, here is the latest info on the issues you brought up:
OMOP Measurement Type should be a separate row it the GitHub table, it will be fixed;
and the HGNC vocabulary is deleted from the VOCABULARY table, technically it does not exist in OMOP now, so the Athena list will be made up-to date. Thank you once again!

1 Like
#6

Friends:

We are going to fix all those things. There will be full transparency about what is where and what is not:

  • Which vocabularies are supported
  • Which of them are not supported (by the Coordinating Center)

With regards to the HGNC: Yes, that is missing. Actually, it is in there indirectly, but in the form of the “OMOP Genomic” vocabulary. Check out the concept class “Genetic variation”. Essentially, these are the HGNC entries, added by the phrase gene variant measurement. You’ll notice that the concept codes are HGNC IDs, and the symbols are the first word in the concept_name. I know, totally obscure. We will bring it all out.

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#7

It’s fixed now, please check: Standardized Vocabularies · OHDSI/Vocabulary-v5.0 Wiki · GitHub

Here’s the GitHub issue.

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