Hello, I deployed Athena locally, but the sorting of returned results are inconsistent when I input the same term name. Take the example of “lymphocyte”:
Athena search results:
Local Athena search results:
Hi, I think Athena search results are still not complete. If I search by “V600E”, Athena returns:
But none of the search results are from VOCAB: OncoKB, which is a match to my search term as well.
cant show the screenshot due to new user restriction, sorry
Anyone know why? Is this a bug that to be fixed? Thanks.
Hi @User1643. The actual concepts you want to map cancer biomarkers like BRAF V600E are in the OMOP Genomic vocabulary. This specific concept is:
BRAF protein: Substitution in position 600 Val replaced by Glu measurement
In the OnkoKB vocabulary it is:
The reason you don’t find it by searching for “V600E” is that Athena doesn’t search partial strings.
But you don’t want to find it in OnoKB anyway since that vocabulary is completely non-standard in OMOP. The standard concepts are in OMOP Genomic.
That said, you also won’t find it by searching for “V600E” in OMOP Genomic because the synonyms for it are:
NP_004324.2:p.V600E
NP_001341538.1:p.V600E
and Athena’s search won’t find those. That is a “bug”. We need to add synonyms for cancer biomarkers that make then findable via common shorthand like “V600E”. That work is underway.
Meanwhile, I find biomarkers like this in Athena by selecting the OMOP Genomic vocabulary and then searching for “BRAF 600 protein”.
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Understood, thanks for the explanation @jmethot
While for cancer diagnosis e.g. “triple negative breast cancer”, I should search by concept = “Standard” and domain = “Condition” in Athena, which “45768522” from SNOMED vocab is the OMOP ID for this condition, right?
Same goes to cancer diagnosis “Infiltrating lobular carcinoma of breast”, OMOP ID for this condition will be “4080865”, is it correct? Thanks.
Yes this is correct if what you mean by ‘OMOP ID’ is the condition_concept _id populated in condition table. In this case condition_source_concept_id will be the same as condition_concept _id.
You can also look at non-standard concepts and check their mapping (some will map to standard concepts with ‘Maps to’ relationship). Then you capture non-standard concept id in condition_source_concept_id field and standard mapped concept id in condition_concept _id. Refer to The Book of OHDSI for the details.
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