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UCUM vocabulary not offered by ATHENA for V5 download


(Gerald Pulver) #1

What am I doing wrong?
I figure that I must be overlooking something painfully obvious, as there must be valid unit concepts in DRUG_STRENGTH.

I get the same results for amount_unit_concept_ID, numerator_unit_concept_ID, and denominator_unit_concept_ID.

2513 proc sql ;
2514 create table test as
2515 select distinct
2516 ds.amount_unit_concept_ID,
2517 c.concept_name
2518 from
2519 v5.drug_strength as ds inner join
2520 v5.concept as c
2521 on
2522 ds.amount_unit_concept_ID = c.concept_ID;
NOTE: Table WORK.TEST created, with 0 rows and 2 columns.

	;

(Christian Reich) #2

All there, @pulver. Did you load the DRUG_STRENGTH table?


(Gerald Pulver) #3

The DRUG_STRENGTH table is loaded. I get the concept codes out of it. I will re-check CONCEPT to see if I am looking at a truncated or otherwise problematic copy.

Thanks


(Gerald Pulver) #4

@Christian_Reich
I believe that I have found the problem.
Athena is not presently offering the UCUM vocabulary for download.
So, its concepts, like

  • ID=8576
  • CODE=mg
  • NAME=milligram
  • CLASS=Unit
  • CONCEPT=Standard
  • VALIDITY=Valid
  • DOMAIN=Unit
  • VOCABULARY=UCUM

are not present in my V5.CONCEPT.

Will it be available again soon?


(Gerald Pulver) #5

I found it on: http://ftp.ohdsi.org/
I had been looking at http://athena.ohdsi.org/vocabulary/list

I see now that http://ftp.ohdsi.org/ has apparently not been updated since 05Feb2018, while http://athena.ohdsi.org/vocabulary/list was last updated on 21Apr2019.

As I doubt the there have been many revisions to the units of measure since last year, as an interim solution, I will try to download UCUM alone from http://ftp.ohdsi.org/ and merge it into what I get from http://athena.ohdsi.org/vocabulary/list.


(Dmytry Dymshyts) #6

UCUM is not shown here, because it is uploaded by default.
You don’t see it in the vocabulary list, but you will see in the CONCEPT table.
I double checked this - uploaded some vocabularies, opened CONCEPT table, and I see the UCUM there.
Can you please download the package one more time and check. If you don’t have UCUM anyway, please forward me ( ddymshyts@odysseusinc.com ) the message from Athena with the link, so I can take a look on your vocabulary package.


(Gerald Pulver) #7

Thank you, @Dymshyts.

The UCUM concepts were not present in the CONCEPT file being used here. When I ordered a new one, it was not listed on my selection menu. I learned this morning, from my colleague who received the new copy, that though not explicitly selected, it is present on the latest download.

I am curious as to why UCUM is not included on the menu, perhaps with a permanent check in its selection box. But that is just a curiosity for me. I don’t need an answer to that.

Best,
Gerry


(Christian Reich) #8

@pulver:

Because it is required by default, and we removed it from the list because it is one of many vocabularies that are small and mandatory, and listing them with a non-editable checkbox would make the page even longer than it already is. But I agree, we should make this more obvious.


(Gerald Pulver) #9

@Christian_Reich
Thanks. I wonder why our incumbent CONCEPT lacked a default vocabulary. No matter; we have it now.


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