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How to populate _concept_id fields in CDM Note table?


(Tatiana) #1

Hello,

  1. I would like to ask you about populating the following fields in the CDM Note table
    -Note_class_concept_id
    -Language_concept_id
    -Encoding_concept_id

How to query the possible values for these fields?
For example, to populate note_type_concept_id field I applied filter on the vocabulary_id = ‘Note Type’ .
2. Also, can we leave note_class_concept_id and encoding_concept_id with 0 values if there is no any specific information on it?

Kind regards,
Tatiana


(Christian Reich) #2

@TBanokina:

Note:

select * from concept where vocabulary_id='Note Type';

But: We are creating a whole hierarchy:

select a.min_levels_of_separation as a_min,
  de.concept_id as de_id, de.concept_name as de_name, de.vocabulary_id as de_vocab, de.domain_id as de_domain, de.concept_class_id as de_class
from concept an
join concept_ancestor a on a.ancestor_concept_id=an.concept_id
join concept de on de.concept_id=a.descendant_concept_id
where an.concept_id=36209248
order by min_levels_of_separation;

We will replace the old one with these soon.

Language:

select * from concept where concept_name like '%language' and vocabulary_id='SNOMED' and concept_class_id='Qualifier Value' and invalid_reason is null;

But you probably need English: 4180186

Encoding and Note Class:

Not sure. We need to ask the folks who own all these changes: @HuaXu, @rimma, @noemie? Please help

I’d leave out or set to 0 for now.


(Seng Chan You) #3

Thank you @Christian_Reich
I was trying to find Language concept id (I thought these concept_id would exist in sort of ‘language’ domain)
I want to know how to find concept_id s for note_class_concept_id and encoding_concept_id, too


(Christian Reich) #4

@SCYou:

Yeah, we need to clean up the domains and have a proper way to link them to fields and tables. Will do.

Korean: concept_id=4175771


How to query for the valid list of possible values for NOTE.encoding_concept_id and NOTE.language_concept_id?
(Ambuj) #5

I am also looking out for answer to this one. Do we have any update on Encoding_Concept_Id. If not, can we use concept_id=0 for the same?


(Christian Reich) #6

@ambuj:

Wait. Aren’t you already discussing this here? Like in “the more often I ask, the more likely I will get it”? :slight_smile:


(Ambuj) #7

Lol, yes I am asking it there too. But not able to come up with an appropriate solution to it, Will it be OK to use encoding_concept_id=0 and notes_class_concept_id=0 ?


(Christian Reich) #8

We’ll give you the UTF-8 concept. In the mean time, yes, use 0.
What is the problem with notes_class_cocnept_id?


(Ambuj) #9

Thank you for your prompt response.
Issue with notes_class_concept_id is how to populate note class for Discharge Summary or Progress note.


(Christian Reich) #10

All there:
Progress Note: http://athena.ohdsi.org/search-terms/terms/706550
Discharge Summary: http://athena.ohdsi.org/search-terms/terms/706531

You can find them all in http://athena.ohdsi.org/search-terms/terms?vocabulary=LOINC&conceptClass=Doc+Type+of+Service.


(Ambuj) #11

Thank you again.
I will discuss it with the team and get back to you on this. :slight_smile:


(Micheal ) #12

Is that all of ‘Note_type_concept’ in CDM Note table?
I counted all of them, there are 123 concepts on Athena.
Please tell me if it’s wrong. Thank you @Christian_Reich


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