Athena LOINC vocabulary fields/attributes not in downloaded tables

General
1

Hello,
I’m quite new to OHDSI, so apologies in advance if the answer is obvious.
After downloading LOINC vocabulary table from Athena, I received the following tables:
concept, concept_ancestor, concept_class, concept_relationship, concept_synonym, domain, relationship.

However, I can’t find the fields found on the LOINC website, as well as the online Athena tool, that includes: Component, System, Property etc.

I see it here on Athena website like I said, but are these not downloadable?

image
image1836×656 51.1 KB

(Athena)

Thanks,

2

Hi @may_a ,
As I understand it, when you select a vocabulary to download, you are simply requesting the OMOP content for concepts in those vocabularies. This is different fron the files you might get when dowloading (or requesting) files generated by the SDO.

We store native files from the SDO on a separate terminology server. Not sure what others do…

@Christian_Reich will have the gold standard for answer to this question.

piper

3

Try running this query

select c1.concept_code, c1.concept_name
, relationship_id
, c2.concept_code, c2.concept_name
FROM concept c1
JOIN concept_relationship ON concept_id_1 = c1.concept_id
JOIN concept c2 ON c2.concept_id = concept_id_1
WHERE concept_id_1 = 3011960
ORDER BY relationship_id

Then look at The Book of OHDSI Standardized Vocabulary, relationships to understand how/why it works.

4

Ah, @may_a I misread your post! I thoght you were asking about the “files” (not fields) found on the LOINC website :crazy_face: :stuck_out_tongue_winking_eye: