OHDSI Home | Forums | Wiki | Github

Using ETL Data to Derive an ICD-10-CM to SNOMED CT Map


(Keith Welch) #1

I am creating a ICD-10-CM map to SNOMED (Yes, I am aware that this will not always yield a 1-1 mapping)

I have been told by a high level informaticist that there are data files referenced somewhere in the OHDSI scope that can be used to create such a map between ICD-10 and SNOMED. This does not have to be a 1-1 map. However, the data set found on

https://www.nlm.nih.gov/research/umls/mapping_projects/snomedct_to_icd10cm.html

can yield up to 1800 SNOMED values per ICD10. This suggests that this is not an optimal dataset.

What specific files could support finding all these relationships?

RKW


(Christian Reich) #2

@keithwelch:

OHDSI provides a mapping from ICD10CM to SNOMED for free through the Standardized Vocabularies. You can read all about things in the Book of OHDSI, but in a nutshell:

  • Create a OMOP database using the DDL available in the Github, but you really only need the tables CONCEPT and CONCEPT_RELATIONSHIP.
  • Download the Vocabularies from Athena and load at least these two tables.
  • Extract the mapping:

select c1.concept_code as ICD10CM_code, c2.concept_code as SNOMED_code
from concept c1
join concept_relationship on concept_id_1=c1.concept_id
join concept c2 on concept_id_2=c2.concept_id
where c1.vocabulary_id=‘ICD10CM’ and c2.vocabulary_id=‘SNOMED’
and relationship_id=‘Maps to’

and voilà.


t