SNOMED concept_id to concept_code

Vocabulary Users
1

When looking at SNOMED concept_id in Athena (Athena), there is a relationship between SNOMED concept_id and concept_code. However, when exporting SNOMED vocabularies, this relationship no longer exists. For example, concept_id 140673 maps to concept_code 40930008 in Athena. I have specifically looked into the ‘CONCEPT’ file.
Does someone know how to map SNOMED concept_id to SNOMED concept_code? Is there a mapping file available?

Thanks!

2

Thank you for raising this question. When mapping, it is usually the process of creating ‘Maps to’ relationships between two concepts. The concept_id is a unique identifier of the concept in OMOP, while concept_code is used to identify concept inside the vocabulary. One concept_code can belong to several concept_ids. For example, concepts with identical concept_code 1001, but with different vocabularies, domains and concept classes.

Links between concept_code and concept_id could be found in concept table, while links between different concepts in concept_relationship_table. Standard concepts may also have ‘Maps to’ relationships to themselves.

You may also refer to this link to the Book of Ohdsi under the chapter on Concepts under Standardized Vocabularies. Chapter 5 Standardized Vocabularies | The Book of OHDSI

3

Thank you so much for the answer @janice.
I still have problems understanding and trusting the “CONCEPT” file. For example, the concept_id 140673 (hypothyreosis) maps to concept_code 40930008 Athena, but not in the “CONCEPT” file. Do you have an explanation for that?

4

Actually it does perfectly:

SELECT *
FROM dbo.concept (NOLOCK) c
WHERE c.concept_id = 140673;
5

Hi @statarat,
I think the confusion here is between the concept_id vs the concept_code. In your example, the concept_code (40930008) is the actual SNOMED code for Hypothyroidism. The concept_id is OMOP’s unique identifier as @janice mentions in her reply.

“Mapping” in OMOP happens with the concept_relationship table using the ‘Maps to’ relationship_id. In your example, this concept maps to itself because it is a standard concept.
SELECT C.VOCABULARY_ID, C.CONCEPT_ID, C.CONCEPT_CODE SNOMED_CODE, C.CONCEPT_NAME, C.STANDARD_CONCEPT
, CR.RELATIONSHIP_ID, CR.CONCEPT_ID_1, CR.CONCEPT_ID_2 MAPPED_CONCEPT
FROM CONCEPT c
JOIN CONCEPT_RELATIONSHIP CR on CR.CONCEPT_ID_1 = C.CONCEPT_ID AND RELATIONSHIP_ID = ‘Maps to’
WHERE CONCEPT_ID = 140673;

6

Thank you so much for the explanation @Tom_Galia. I appreciate it.