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OHDSI / Vocabulary-v5.0

Build process for the OHDSI Standardized Vocabularies. Currently not available as independent release.
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RxNorm deprecated concepts without mappings to Standard #372

Open cukarthik opened 6 years ago

cukarthik commented 6 years ago

We are using the most recent vocabulary (v5.0 15-DEC-17) to populate our OMOP instance, and we noticed drug concept ids that are in our dataset that are do not map to a standard concept id. I've attached the full list of codes that are missing and their frequency in our data. Thanks. drugs_missing_standard_mappings.xlsx

cgreich commented 6 years ago

@cukarthik:

Looks like these are all those where RxNorm deprecated a concept without giving a successor, and NDCs and Multums lost their mapping target. The reason for this is they either revised the Dose Form (e.g. injectable solution to injection), the dose (concentration in injectable solution to total amount in injection) or the ingredient. When they did that, they re-mapped NDCs to the new concepts but didn't bother with the old ones.

We need to come up with a fix for these.

aostropolets commented 6 years ago

@cukarthik Christian is right. Will take a closer look after holidays to come up with a nice solution.

cukarthik commented 6 years ago

@aostropolets just wondering if we were able to clean this up a little? Thanks.

aostropolets commented 6 years ago

Ah! Thanks for the reminder. We need to develop a logic for these RxNorm codes. Promise to take a look next week

aostropolets commented 6 years ago

@cukarthik small update while I'm working on the list: you have 2 Precise Ingredients 19026600 and 19082770. They are non-standard as their standard counterparts are regular ingredients: 1551860 and 1510813 respectively; with the relationship_id = 'Form of'

cukarthik commented 6 years ago

So for these cases we should to use the "Form of" relationship? Just curious, is there a reason why it couldn't also be part of the "Maps to" relationship?

cgreich commented 6 years ago

It could, @cukarthik. We'll add.

dimshitc commented 5 years ago

@aostropolets where are we with this?

aostropolets commented 5 years ago

I think some of the mappings are there. But, of course, you'd better check and see.

cgreich commented 5 years ago

Can we fix them all systematically?

Alexdavv commented 4 years ago

Some more RxNorm concepts unmapped: https://github.com/OHDSI/Vocabulary-v5.0/issues/277#issue-565008014 https://github.com/OHDSI/Vocabulary-v5.0/issues/239#issue-466400458

cukarthik commented 3 years ago

@Alexdavv @cgreich is this ticket address with the above two tickets?

cgreich commented 3 years ago

Not the same, but related. We are fixing the drug mapping machinery.