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Difference between SPECIMEN_CONCEPT_ID and SPECIMEN_TYPE_CONCEPT_ID


(Vimala Jacob) #1

Hello,

I am about to load data into the SPECIMEN table. As I understand, the SPECIMEN_CONCEPT_ID column is indicate where the specimen was obtained from, such as a blood or tissue sample. So what would we insert into the SPECIMEN_TYPE_CONCEPT_ID column?

Regards,
Vimala


(Don Torok) #2

Select * from concept where domain_id = ‘Type Concept’ and concept_class =
‘Specimen Type’. Looks like only one choice ‘EHR Detail’


(Vimala Jacob) #3

Hello Don,

Thanks for your reply. However when I ran the query you provided, it did not return any rows. What version of the CDM did you run your query against?

I am using v5.0.

Here is the result of my query:

select * from concept where domain_id=‘Type Concept’ and concept_name like ‘EHR De%’ order by concept_name;
concept_id | concept_name | domain_id | vocabulary_id | concept_class_id | standard_concept | concept_code | valid_start_date | valid_end_date | invalid_reason
------------±-------------±-------------±--------------±-----------------±-----------------±---------------±-----------------±---------------±---------------
44818707 | EHR Detail | Type Concept | Device Type | Device Type | S | OMOP generated | 1970-01-01 | 2099-12-31 |

Regards,
Vimala


(Dmytry Dymshyts) #4

For version 5.0 you use this query:

Select * from concept where domain_id = ‘Type Concept’ and concept_class_id = ‘Specimen Type’

there’s a typo - should be “concept_class_id” instead of “concept_class” (seems you confused with 4.5 version)

so you should get such a result (exactly as @DTorok said)
581378 EHR Detail Type Concept Specimen Type Specimen Type S OMOP generated 1970-01-01 00:00:00.0 2099-12-31 00:00:00.0


(Vimala Jacob) #5

Hello Dmytry,

I did try your query before to no avail. Can you think of a reason why that might be the case?

Regards,
Vimala


(Dmytry Dymshyts) #6

Maybe you use some of the old versions of the vocabulary.
please, download the latest release of OHDSI-vocabularies from Athena
http://athena.ohdsi.org/


#7

Hi,

I have been trying to download the vocabulary from this Wednesday, but I have not been able to download it until now.
After logging at the Athena homepage, even if you click the Download tab, only the login screen is displayed.
Please let me know how to do.

thanks.


(Dmytry Dymshyts) #8

yeah, there is a log-in pop-up, but the main window shows you the registration option.

Can you see it?


#9

Thank you. I downloaded it from another computer.
But I still can not log in on my laptop…


(Dmytry Dymshyts) #10

What browser do you use?


(Micheal ) #11

Hello @Dymshyts
I already downloaded V6.0 Vocabularies, but there is still no Specimen data…
Could you recommend the solution?


(Doyeop Kim) #12

Aren’t there specimen_concept_ids in the vocabulary downloaded from Athena?


(Dmytry Dymshyts) #13

select * from concept where domain_id =‘Specimen’ and standard_concept =‘S’;
it’s the list of concepts can be used as SPECIMEN.specimen_concept_id.


(Micheal ) #14

Thank you @Dymshyts


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