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Starting Usagi with CIEL vocabulary

Vocabulary Users
#1

Hi there, I am trying out Usagi to see if I can match a sample CSV concept file specifically to the CIEL vocabulary, which I downloaded from Athena. I am able to set up the program and run it properly, but I am struggling to make the matching work. It seems as if Usagi does not recognize that CIEL is present in the Vocabulary download folder, even though I can see CIEL in the “VOCABULARY.csv” file.

Is there a sort of Getting Started guide to using Usagi specifically to match to a non “out-of-the-box” vocabulary? I could not find instructions to make another vocabulary like CIEL appear in any of my mapping or search results. Even the “Filter by vocabulary” dropdown menu does not include CIEL.

Including a screenshot of how far I’ve gotten. The concepts “Yes” and “No” are good examples of concepts that CIEL should have, but it is not appearing in the search results (including the upper and lower lists on the screen).

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#2

Hello @jamlung and welcome to OHDSI!

Two things to note:

  1. You don’t need to use Usagi to map source codes to OHDSI supported vocabularies. And CIEL is an OHDSI supported vocabulary. See the Book of OHDSI to learn how to map these data.

  2. When you use Usagi, it will present you target matches which are standard concepts. The CIEL vocabulary does not contain any standard concepts. Thus, you don’t see these as targets.

1 Like
#3

Ah okay, thank you @MPhilofsky! That helped me figure out how best to try out Usagi with CIEL since I wanted to see what its capabilities are.

In case this helps anyone else, I changed all CIEL concepts in the CONCEPTS.csv file to have a value “S” in the Standard concept field, which opened up CIEL concepts to be possible match targets for Usagi.

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