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Concept tables work in progress? How to get on the list for new release?

Vocabulary Users
#1

My general question is that if the concept tables are still work in progress? I assume many of them are. Specifically, I am looking at the concept_relationship table for ‘cross walking’ between vocabularies. The only cross walking I can find is 2000+ entries between LOINC and CPT. Is there plan to add other cross walk such as ICD9 - ICD10, ICD10 - SNOMED?
How do we users get update when there is new release on any of the concept tables?

select concept_id_1, domain_id, vocabulary_id, concept_name, concept_id_2 from concept_relationship , concept where concept_id_1 = concept_id and relationship_id = ‘LOINC - CPT4 eq’

FYI: relationship_id = relationship_id ‘maps’ was my first instinct to query, but it does not serve the crosswalk between vocabularies, but similar to another relationship_id ‘concept replaces’ from my understanding --for deprecated concepts. Can someone clarify the difference?

#3

@yulingjiang:

There are tons of crosswalks in the Vocabularies. But the point is not to just accumulate random crosswalks, but instead create mappings between non-standard (=source) and standard Concepts as described here. So, there is no point in ICD9-ICD10 (which really is ICD9CM-ICD10CM) crosswalks, both contain exclusively source concepts. There are tons of ICD10CM-SNOMED mappings.

The relationship_id is called “Maps to”. However, it also contains mappings within vocabularies from deprecated or source concepts to standard ones. However, there are plenty of other relationship_ids creating equivalents between concepts from different vocabularies (ATC - RxNorm eq, Source - RxNorm eq etc.). But again, their purpose is to support automatic building of Maps to relationships.

For updates sign up here. Click on Watch. Hope this helps.

#4

@yulingjiang:

If you are coming to the 2017 OHDSI Symposium, feel free to sign up for the CDM and Vocabulary Tutorial sessions. You’ll learn it all.

#6

Thank you! They look like great tutorials, exactly what I need. Has the registration opened yet?

#7

Thanks for the answer in detail. Excuse my basic questions, I am looking forward to the tutorial to learn more. My query or “Maps to” didn’t return the ICD10CM-SNOMED mappings, or anything when I exclude the ‘self mapping’ of Standard concept and the deprecated concepts. Did I not get it right? Do you have a query or some example returns of the ICD10CM-SNOMED mapping?

select concept_id_1, concept_id, domain_id, vocabulary_id, concept_name, concept_id_2 from concept_relationship r, concept c where concept_id_1 = concept_id and relationship_id = ‘Maps to’ and concept_id_1 <> concept_id_2
and concept_id_1 not in (select concept_id from concept where invalid_reason is not null)
and concept_id_2 not in (select concept_id from concept where invalid_reason is null);

#9

@yulingjiang:

Will open any minute now.

Here is the query to get ICD10CM to SNOMED mapping:

select c1.concept_id as c1_id, c1.concept_name as c1_name, c1.vocabulary_id as c1_vocab, c1.domain_id as c1_domain, c1.concept_class_id as c1_class,
  c2.concept_id as c2_id, c2.concept_name as c2_name, c2.vocabulary_id as c2_vocab, c2.standard_concept, c2.concept_class_id as c2_class
from concept c1
join concept_relationship r on r.concept_id_1=c1.concept_id and r.invalid_reason is null and r.relationship_id='Maps to'
join concept c2 on c2.concept_id=r.concept_id_2
where c1.vocabulary_id='ICD10CM';
#10

@Christian_Reich
Thanks! I will keep an eye on the registration.
I could not get any return with your query either. Also tried modifying query to look backward (where c2.vocabulary_id = ‘SNOMED’), still nothing. There are multiple entries in concept for both ‘ICD10CM’ and ‘SNOMED’, but can’t find their mapping through concept_relationship. Did I miss some important point here?

#11

@yulingjiang:

When you downloaded the vocabularies, did you click ICD10CM? I know it’s a silly question, but that is the most common version. Because I tested the query before copying it in here.

#12

@Christian_Reich:
Not silly questions at all. That was exactly first thing I wanted to check when there were no returns. I remember checking ‘ICD10CM’ when submitting request 2 months ago, not quite sure about ‘SNOMED’. So I queried my concept table for both ‘ICD10CM’ and ‘SNOMED’, there are entries for both. This should mean I had downloaded both vocabularies. But would it be different for the concept_relationship table?

select * from concept where vocabulary_id=‘ICD10CM’;

select * from concept where vocabulary_id = ‘SNOMED’;

#13

In the meanwhile, I am requesting the concept tables again to make sure both vocabularies are checked.

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