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Help regarding mapping to drug_exposure

Developers
#1

I’ve been trying to map the medications table from a healthcare database to OMOP’s drug_exposure table. I stumbled upon some queries that have been provided by the forum: http://vocabqueries.omop.org/drug-queries/d2
I am facing two problems. I observed multiple mapping for medications, e.g. Lipitor (given in the example) is mapped to 7 rows in OMOP where the change is in the units. Any help on how to proceed is appreciated.
Also, the query addresses CONCEPT_SYNONYM table. But I haven’t been able to find it. Please let me know where I can find the vocabulary for synonyms.

#2

@omop_cdm:

(You may pick a better name on this forum. Unless your first name is OMOP and last name is CDM. :slight_smile: )

Are you trying to convert your data into OMOP CDM, or are you trying to query the resulting CDM database? Where are you?

#3

I am trying to convert my data into OMOP CDM format. I have been able to map conditions and patient details. But, I am stuck in medications. The database I am trying to map has medications stored in form of labels and not codes. When I try to map these labels like Lansoprazole or Lipitor to OMOP vocabulary, it returns multiple mappings.
For e.g. for ‘Lipitor’, it returns 7 rows.

1545998 | atorvastatin 10 MG Oral Tablet [Lipitor]
1545999 | atorvastatin 20 MG Oral Tablet [Lipitor]
19068781 | atorvastatin 80 MG Oral Tablet [Lipitor]
19123593 | atorvastatin 40 MG Oral Tablet [Lipitor]
40095235 | atorvastatin 10 MG Oral Tablet [Lipitor]
40095238 | atorvastatin 20 MG Oral Tablet [Lipitor]
40095241 | atorvastatin 40 MG Oral Tablet [Lipitor]

I want it to map only to a single value only. How can I change this?

Thanks a lot!!

1 Like
#4

If you only have Lipitor you don’t really know which of hte products was given. Only the brand name (trade name) of the active compound. So, you find the brand name:

select * from concept where lower(concept_name) = ‘lipitor’ and vocabulary_id=‘RxNorm’.

You’ll get the concept with the concept_id=19023381 back. Then you find the active ingredient thereof:

select * from concept join concept_relationship on concept_id_1=concept_id
where concept_id_1=19023381 and concept_class_id=‘Ingredient’

You get two concepts back, of which one is deprecated. The one you want is the other one: concept_id=1545958 for Atorvastatin.

Let me know if this helps.

1 Like
#5

What type of data source are you using (e.g., EMR, self-reported data,
etc)? Might want to share some rows so people here can see what you’re
working with.

Also, for clarity please change usernames / re-register under a different
username because omop_cdm is a ‘keyword’ if you will.

Thanks,
Jon

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