I have downloaded the vocabulary files for a single vocabulary.
Looking in the CONCEPTS.csv file, there are many concepts included there that are in vocabularies other than the single vocabulary that I selected.
I was expecting that all concepts in CONCEPTS.csv would be either:
* members of the requested vocabulary
* found in CONCEPT_RELATIONSHIP with a defined relationship to a term in the selected vocabulary
* used as a foreign key in
VOCABULARY.vocabulary_concept_id,
CONCEPT_CLASS.concept_class_concept_id,
RELATIONSHIP.relationship_concept_id,
DOMAIN.domain_concept_id
one of [‘drug_concept_id’, ‘ingredient_concept_id’, ‘amount_unit_concept_id’, ‘numerator_unit_concept_id’, ‘denominator_unit_concept_id’] in DRUG_STRENGTH
I can see lots of terms in the CONCEPTS.csv file that do not meet one of the above criteria. They all appear to be either a standard concept, metadata, or belong to the Visit or Observation domain. I wasn’t able to find it in the athena documentation, so can someone confirm - are all of these concepts extracted with every athena extract by definition?