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Local custom concepts vs Published OMOP concepts

Vocabulary Users
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#1

Hi Folks,

I know that we can create local/custom concepts (> 2B concept_id) for our source terms which aren’t found in OMOP vocabularies.

But I also read that the OHDSI Vocab team can consider adding our concepts to OMOP vocabularies if they find it to be useful for a larger community. I guess there is a formal process for it.

My question is

  1. We have a list of concepts from our site which are very specific to our institution’s data collection approach. So, we stick to custom concepts here (>2B concept ids). simple and nothing much can be done here.

  2. What if I find out that those custom concepts created for our site could potentially be used across institutes in our country? Does it stand eligible to be published as a part of OMOP vocabulary? Any other eligibility criteria here?

  3. Let’s say for q2, OMOP doesn’t accept to publish our vocabularies (because it doesn’t help institutes from multiple countries), then we are supposed to exchange our custom concepts vocab files within institutions in our country. Is this how it works? Have I understood it right?

Can someone guide me on this?

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#2

Hello!

If there is a separate curated classification system that is required by multiple institutions it may be added as a new vocabulary to OMOP even if it is country specific. As example, we already have local versions of ICD (American, Korean and Chinese) and numerous drug classifications (UK’s dm+d, Belgian GGR, Japanese JMDC and many others).

Usually if classification is tidy, useful and if license allows it, there are no restrictions for it to be added to OMOP. If the classification has external mappings and (preferably) English translation, it can happen very quickly.

There is no formal process to request a new vocabulary. You could create a new forum post with request, mail our team members or even simply post it in this thread.

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#3

Hi @Eduard_Korchmar,

I have the same question. For ex, in our data, we have created survey questions and answers as custom concepts (for terms which aren’t covered by existing OMOP concepts). However, these could be used by other institutes in our region as well.

The survey questions and answers would focus on socio-economic status, lifestyle behaviors, food habits etc.

Though we have mapped to some existing OMOP vocabs, I couldn’t map few and we created custom concepts.

Can we publish that in OMOP vocab, so other institutes from my region could use it?

If yes, can you let me know what is required from my end and to which email-id, I have to share the relevant files?

Thanks
Selva

#4

Hello @SELVA_MUTHU_KUMARAN ,

You could send everything you have (concepts and mappings) to my e-mail in my profile, I will forward it to our team members and we’ll come up with a way to process it further.

If there is a publicly available updated database for these questions-answers pairs, that would be even better.

#5

Hi @Eduard_Korchmar,

I can put it up in google drive and share the link here? Will that work with you?

btw, I couldn’t find your email-id in profile. I see this Terminologist @ Odysseus Vocabulary Team

If you are okay with me e-mailing the contents (3 csv files), can I kindly request you to let me know your email id?

#6

Link will work well. My e-mail is eduard.korchmar[at]odysseusinc.com

#7

@SELVA_MUTHU_KUMARAN
Or you might just post the files here, so it will be available publicly.

We are working on couple of projects related to surveys, so your list might be handy.

#8

@Dymshyts @Eduard_Korchmar

Apologies for the delayed response. I did drop an email to Eduard.

However, I am attaching the Questionnaire here for the benefit of community.

From page 11, you can see that we have 3 questionnaire instruments such as MMSE, RBANS and GDS

When I manually searched in ATHENA, I was able to see that GDS was already present. However, I couldn’t find other two.

Do you need our custom concept_ids as well (> 2billion)?

Your help/guidance is much appreciated

Selva_Singapore_Questionnaire_MMSE_RBANS_GDS.pdf (964.7 KB)

#9

Hi,

Just to clarify that I do see all the questionnaire names in ATHENA such as MMSE, RBANS and GDS`.

Though for GDS, I am able to find the questions as is but for the other two, the questions that come under each survey instrument are missing or differently represented. Ex: A patient is being asked to draw a rectangle figure which was shown to him. So the question was Is patient able to recall a rectangle figure but in ATHENA, I see certain terms which are like Able to recall a random address within 5 minutes etc.

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