Availability of all standard concept_ids on the mapper

[erummas]

Is there an existing issue for this?

• I have searched the existing issues

Is your proposal related to a problem or functionality gap?

In OMOP the user is only aware of the source vocabulary. It is particularly difficult to see missing mappings for partially mapped source codes. For example I mapped read code 65EB.00 which maps to concept_id 44792015 (SNOMED) and 40213186 (CVX). Since CVX is not supported on mapper currently this concept failed to show in the rules. I have just been made aware that this is incomplete mapping. There are many other codes showing similar behaviour. It is impossible for the user to know this. The only case where it is obvious is when there is no mapping showing at all.

Describe your proposal

It is very hard for the user to know instantly that there are missing partial mappings. My suggestion to counter this, irrespective of the vocabulary all standard concept_ids made available on the mapper. Or list of vocabularies which contain standard codes be fully imported.

Describe alternatives you've considered

No response

I'm part of a Project Team

No response

Anything else?

No response

Are you willing to contribute to developing this feature?

None

[AndyRae]

Hi @erummas - thanks for this.

Yes an aside - it's in our general plan this year to make it easier to understand the visibility/navigating mappings.

Just to be sure I understand - a short solution of this is to provide all standard vocabs in Carrot?

[erummas]

Hi @AndyRae, easier solution would be to make all the vocabularies on Athena be made available, downside is that it would require more space on DB. Another solution could be to have full set of current vocabularies (as they are commonly used) and import only standard (S) concept_ids and their associated records from the remaining vocabularies.

[AndyRae]

Thanks - yes my intention was to make all vocabularies available based on the August update, but their data integrity is inconsistent with the CDM. At this point - I'm thinking we wait until the February update, and try again, would that work for your timeline?

[erummas]

Thank you @AndyRae, that sounds good. Would that be at the end of this month or earlier? I will be needing vocabularies specifically for cancer terms for the dataset I am currently working on. Would be nice to have all vocabularies available on the mapper.

[AndyRae]

@erummas OHDSI do seem to make it the end of the month by the looks of it.

If that's not ideal and you'd prefer it sooner - likely would be this time next week.
I think I'd prefer that, as if it's the end of February when it is released, it means March work for our team which is likely not possible.

[erummas]

Thank you @AndyRae, earlier works for me too.