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OHDSI / OMOP-Standardized-Vocabularies

This repository is not longer active. It used to have the only purpose of creating releases of the Standardized Vocabularies, i.e. the content, not those of the Pallas Vocabulary Build System itself. As of 17-July-2018, vocabulary releases are also processed by Pallas. Please visit https://github.com/OHDSI/Vocabulary-v5.0/releases.
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Concept Class CPT4? #13

Closed PRijnbeek closed 6 years ago

PRijnbeek commented 6 years ago

Why is concept_class 'CPT4' still in the latest vocab? for example concept_id = 2213225

This should not be in there anymore correct according to the wiki correct?: https://github.com/OHDSI/CommonDataModel/wiki/CONCEPT_CLASS

cgreich commented 6 years ago

Why not? We have three concept classes in the CPT4 vocabulary:

It's all good. What do you think the problem is?

aostropolets commented 6 years ago

I believe Peter’s referring to the wiki page, which says that in v5 concept_class_id CPT-4 was changed to Procedure

PRijnbeek commented 6 years ago

Indeed. I read that as if this should not be a concept_class anymore.

It is also to me strange to give the concept_class the name of a vocabulary considering this sentence:

"The CONCEPT_CLASS table is a reference table, which includes a list of the classifications used to differentiate Concepts within a given Vocabulary"

CPT4 itself is not a classification system so I think it should not be the name of concept_class?

"Procedures" would make much more sense to me, as is what is written on the wiki-page.

By the way, it is somewhat strange still that concepts in the Measurement domain can have a concept_class "Procedure", but I understand that these are procedures that have a result...?

aostropolets commented 6 years ago

The thing is that the procedural nature of CPT concepts is represented by their domain_id and most of the concepts apriori are procedures. We use concept_class_id ‘CPT4’ here in order to distinguish between the ordinary CPT4 concepts, hierarchical concepts and modifiers, although all of them belong to procedures.

“By the way, it is somewhat strange still that concepts in the Measurement domain can have a concept_class "Procedure", but I understand that these are procedures that have a result...?” Yep. They mean that you’be done a procedure like, for instance, microscopy, culture etc. in 4057441 Identification of microorganisms in CSF, but you still can put into an actual result.

cgreich commented 6 years ago

Well, the thing is that the documentation is way behind, and we have been procrastinating fixing it up for a long time, really. (Scratching egg off face).