Two standard concepts for concept_id 45576364

[ssanghani1]

Hello Everyone,

I have just started learning OMOP. I am super excited to learn it and attend the upcoming symposium.

I came across concept_id 45576364 that links to two standard concepts, both are valid (without valid_end_date) and have same valid_start_date. Not sure which one should I use.

This is the query I am using:

select c_scr., '’ as Divider, cr., '**’ as Divider, c_tar.
from concept c_scr
join concept_relationship cr on c_scr.concept_id = cr.concept_id_1 and cr.relationship_id = ‘Maps to’
join concept c_tar on cr.concept_id_2 = c_tar.concept_id and c_tar.standard_concept = ‘S’
where c_scr.vocabulary_id in (‘ICD10’,‘ICD10CM’)
and c_scr.concept_id = 45576364

I would greatly appreciate if someone can guide me how to determine which standard concept_id should I use.

Thank you!

[ssanghani1]

I am sorry, the query did not paste properly in the original post

This is the correct one:

select c_scr., cr., c_tar.*
from Concept c_scr
join concept_relationship cr on c_scr.concept_id = cr.concept_id_1 and cr.relationship_id = ‘Maps to’
join concept c_tar on cr.concept_id_2 = c_tar.concept_id and c_tar.standard_concept = ‘S’
where c_scr.vocabulary_id in (‘ICD10’,‘ICD10CM’)
and c_scr.concept_id = 45576364

[esholle (Evan Sholle)]

This thread may be relevant for you:

concept_id maps to more than one concept_ids on the concept_relationship table of the OMOP CMD standardized vocabulary

Hello! I am writing to ask why do some concept_ids on the concept_relationship table map to more than one valid value. Please find an example in the screenshot below. [image] I thought each concept_id maps to exactly one standard and valid concept_id. Please correct me if I am wrong. For the record, last time I updated my concept_relationship table from Athena was the 2nd of July 2018. I would deeply appreciate your assistance!

As per @Chris_Knoll there, the appropriate course of action is to map to both, unless I’m grossly misunderstanding. For more information about circumstances where one non-standard source value maps to multiple standard concepts, see the mapping rules: documentation:vocabulary:mapping [Observational Health Data Sciences and Informatics]

[mvanzandt (Mui Van Zandt)]

Yes, you would map them to both, which means you will end up with two OMOP condition_occurrence records for the 1 source record. This can happen because ICD codes are not always describing just one diagnosis. Sometimes it combines multiple diagnosis into one.

For this ICD term, it is both Malignant lymphoma of lymph nodes of multiple sites and Non-Hodgkin’s lymphoma.

[ssanghani1]

Thank you very much Evan and Mui! I totally appreciate your help.

[Christian_Reich]

You still didn’t paste properly, but good enough.

Yes, this is a complex ICD10: Non-Hodgkin lymphoma of multiple sites of lymph nodes. There is no exact equivalent in SNOMED, and hence it got mapped to the first half and the second half: Nothing else we can do today, but we are planning to introduce those combo-concepts as SNOMED Extensions and then line them up correctly into the existing SNOMED hierarchy. This will fix this problem. But we are now talking to SNOMED about the pros and cons of doing something like that (vs having them do it).

Till then, please map to both Concepts and write them both into the CONDITION_OCCURRENCE table.

[ssanghani1]

Thank you very much Christian. I appreciate your reply.