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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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Trastuzumab Emtansine incorrectly mapped to Trastuzumab #169

Open abedtashh opened 6 years ago

abedtashh commented 6 years ago

Probem:

"Trastuzumab" and "Trastuzumab Emtansine" are two different ingredients, but Trastuzumab Emtansine in GRR, BDPM, and dm+d vocabularies are mapped to RxNorm concept of Trastuzumab (Concept ID: 224905):

RELATES TO CONCEPT ID VOCABULARY
Trastuzumab Emtansine 41605044 GRR
Trastuzumab emtansine 43243659 BDPM
Trastuzumab emtansine 21309257 dm+d
Trastuzumab emtansine 21234907 dm+d
Trastuzumab emtansine 21179199 dm+d

Suggestion:

The above 5 concepts need to be mapped to RxNorm concept of ado-trastuzumab emtansine (43525787).

cgreich commented 6 years ago

True. Will fix.

ericaVoss commented 6 years ago

Testing in 20180609

I don't have GRR since @cgreich won't let me have it . . . but . . . 

WITH CTE_DRUGS_OF_INTEREST AS (
    SELECT *
    FROM CONCEPT
    WHERE CONCEPT_ID IN (
    41605044,43243659,21309257,21234907,21179199
    )
)
SELECT i.CONCEPT_ID, i.CONCEPT_NAME, i.VOCABULARY_ID, c.CONCEPT_ID, c.CONCEPT_NAME, c.CONCEPT_CLASS_ID
FROM CTE_DRUGS_OF_INTEREST i
    LEFT OUTER JOIN CONCEPT_RELATIONSHIP cr
        ON cr.CONCEPT_ID_1 = i.CONCEPT_ID
    LEFT OUTER JOIN CONCEPT c
        ON c.CONCEPT_ID = cr.CONCEPT_ID_2

Still being mapped to 1387104-trastuzumab

cgreich commented 6 years ago

Aren't you guys buying DA GErmany? That's what it is in tehre. You can have it.

ericaVoss commented 6 years ago

YES, we have DA Germany!! But you refuse to approve my permissions to it.

See #137

bitmoji

abedtashh commented 6 years ago

I just checked Athena. Not fixed yet!

There is a shortcut to see which concepts need to be changed: All "Trastuzumab emtansine" concepts that are incorrectly mapped to "Trastuzumab" RxNorm concept (here: http://athena.ohdsi.org/search-terms/terms/1387104) need to be mapped to "ado-trastuzumab emtansine" RxNorm concept (http://athena.ohdsi.org/search-terms/terms/43525787).

aostropolets commented 6 years ago

Hamed, it’s not that easy as you think. We need to update and refresh all the vocabularies that are involved. It apparently takes time and resources. We will do it as soon as possible. Will keep you posted.

deepakyedlarajaiah commented 8 months ago

Please advise if this issue has been fixed.we are encountering the same issue.

TinyRickC137 commented 3 weeks ago

@deepakyedlarajaiah it has not been fixed yet - to fix this problem, we need to change the logic of drug processing in OMOP completely. RxNorm is a foundation of a Drug domain in OHDSI, and RxNorm treats trastuzumab emtansine as a precise ingredient (a form of an ingredient and not a distinct concept). There are multiple drugs with the same problem.

Currently, we work according to the roadmap, and the plan is to fix the condition domain first (almost done), then switch to drugs. I will expect changes in the upcoming years, but it is like a change of the whole foundation of the building - not easy at all.