Are there any recommendation on how to map NAACCR ‘Tobacco Use Smoking Status’ and ‘Alcohol Use Status’ to CDM, and whether / what to record as source_concept_ids?
Thank you,
Hannes
We will produce the NAACCR mapping soon.
I’ll stay peeled. Thank you!
@Christian_Reich it’s not about mapping only.
We have to update NAACCR in OMOP, since there are no such a concepts in Athena.
On the other hand, I can find ‘Tobacco Use Smoking Status’ in NAACCR DATA DICTIONARY, but can’t find the ‘Alcohol Use Status’,
@hannes can you please post the item_number for ‘Alcohol Use Status’ you use.
@Dymshyts Good catch. I found the ‘Alcohol History’ field in the dataset I have been working with. The item number is #350. However, I just found out that this item was retired in 2010. I did not find any rationale why. I have listed the observed values in the dataset below, though I think the request is now moot.
0 - No History of Alcohol
1 - Current Use of Alcohol
2 - Past History of Alcohol
9 - Alcohol Usage Unknown
Is this code widely used later than 2010 in your dataset?
It is a tumor registry with 60K records. Here are the record counts with Alcohol History for the years post 2012.
| Year | Record Count with #350 |
|---|---|
| 2011 | 4894 |
| 2012 | 4816 |
| 2013 | 4811 |
| 2014 | 5255 |
| 2015 | 5702 |
| 2016 | 5196 |
| 2017 | 5255 |
| 2018 | 5352 |
| 2019 | 4994 |
| 2020 | 8341 |
| 2021 | 60 |
| Total: | 54676 |
The low record count for 2021 reflects the typical lag in reporting.
Hm, seems those who filled the registry weren’t aware that this code was retired:)
Or they were, but as NAACCR doesn’t provide a replecament code, they used this one out of despair.
Anyway, when we do the NAACCR update we’ll map it to some more reliable terminology like SNOMED or LOINC.
Thank you.
Hey everyone,
I came across this post and was wondering if there are any updates on the alcohol status question and its possible answers. We’re working on an EHR system using FHIR standards, intending to map the data to OMOP on the fly. To do that, we need to assign proper, preferably standard, codes to the questions and their answers. One example that we have used is:
- Tobacco smoking status [Athena]:
- Current every day smoker
- Current some day smoker
- Former smoker
- …
One of the questions is about alcohol consumption, with answers ranging from daily consumption to no consumption. I haven’t been able to find a code that fully captures this range or something similar to the above for alcohol. If anyone could point me to a code that fits, or suggest how to model this to align with OHDSI standards if no such code exists?
Thank you in advance!
Hi @rgand!
These problems are not solved by the external terminologies, so they require an OMOP-made solution, as do many others.
Even though the documentation is not perfect, the smoking status problem was actually solved, so you can find more information here:
- [2022 US Symposium] #65 - Smoking Conventions
- Proposal for new Smoking conventions - please weigh in
- OHDSI/Vocabulary-v5.0/Upcoming-changes/smoking-hierarchy
- Release notes v20230116_major/What’s New/ OMOP Extension/Smoking hierarchy
The alcohol use problem is far from being solved. You’ll find a constellation of Standard concepts across various vocabularies, semantic flavors, and modeling approaches (pre-coordination vs post-). However, I can’t recommend using any of them. We need to plan another sprint to solve the problem.