Hi everyone,
I think I have found an issue about the ATHENA vocabularies but I am not sure if I should report it here.
It seems that all the concept_ancestor records involving ‘MedDRA’ ancestor_concepts_ids and standard descendant_concepts_id in the Condition Domain have been removed in the lasts vocabulary versions from ATHENA. The following query do not show any result in which c2.vocabulary_id is different than ‘MedDRA’ when using vocabulary versions v5.0 31-OCT-22 and V5.0 23-JAN-23 whereas it did when using v5.0 16-DEC-21.
select c.concept_class_id, c2.concept_class_id , c2.vocabulary_id , count(*) from concept c inner join concept_ancestor cr on cr.ancestor_concept_id =c.concept_id inner join concept c2 on c2.concept_id = cr.descendant_concept_id where c.vocabulary_id like ‘MedDRA’ and c2.standard_concept in (‘C’ ,‘S’) group by c.concept_class_id, c2.concept_class_id , c2.vocabulary_id order by c2.vocabulary_id ;
In the case of the classification vocabulary ‘ATC’ in the drug domain, there exist concept_ancestor records involving ATC concepts as ancestors_concepts_id and RxNorm, RxNorm Extensions and HemHonc descendant_concepts_ids. I used the same query after replacing the constrain "c.vocabulary_id like ‘MedDRA’ " with "c.vocabulary_id like ‘ATC’ ".
In my case, this impacts the visualization of the condition’s Treemap in ATLAS as hierarchical organization of the conditions is not available. I am not sure if this happens to everyone. If not maybe there is an issue with the MedDRA license but I think that is unlikely as the MedDRA concepts in my concept and concept_relationship tables are ok.
Could you check this query in the current ATHENA vocabularies and in a former version?
Thank you in advance.
Best regards,
Juan Manuel Ramírez