Vocabulary v5 hierarchy

Implementers
1

Hi all,

Does anyone have a tool that allows hierarchical navigation of the v5 vocab? Or perhaps an explanation of the expected top-level concepts?

We’ve imported the v5 data into our tooling but have thousands of top-level concepts, so we’re apparently doing something very wrong.

Thanks!

2

We are working in putting the V5 vocabulary into our MED browser just to see how it feels to use that hierarchy tool, but we are some weeks off from that. George

3

@Brandon_Ulrich:

What about Hermes?

Want to take a look together? You should have very few top-level ones.

4

I’m Brandon’s colleague, continuing the conversation of his behalf.

We have tried Hermes, but couldn’t find a way to browse the concepts based on the overall hierarchy, e.g. in a tree. Are we missing something?

You wrote that there should be very few top-level concepts, could you provide a list of those to make sure that we are on the same page?

We have no problems following the hierarchy defined in the CONCEPT_ANCESTOR file, but it’s not clear to us what constitutes a top-level concept. Simply filtering for valid non-source concepts that don’t have any ancestors results in thousands of concepts. We have also tried to use the domain concepts as top-level concepts, but this still results in thousands of concepts directly underneath some of the domains, e.g. Drug, Procedure, etc. Using the vocabularies themselves as top-level nodes could work, but to me that would seem to defeat the purpose of the unified OMOP vocabulary.

Thanks,
Zsolt

P.s.: I’m not sure why but my post was immediately marked as spam.

5

We have un-spammed it. Not sure what happened there.

6

@zstorok:

You just write like a spammer. Sorry. :smile:

Hermes doesn’t support the hierarchies explicitely. It shows you the relationships, and some of them are hierarchical, but it doesn’t really show you that well. Want to take a look directly on the tables together?