Hello,
I am very new to OMOP and i wanted to ask if anyone could point me in the direction of OMOP resources that map between vocabularies (for example NDC to RxNorm or ICD10 to SNOMED).
Thanks.
You can download the vocabulary and mapping data using the ATHENA tool (link below).
How it works:
Data Model conventions
FAQ to this question (#11)
Relevant tables:
CONCEPT
CONCEPT_RELATIONSHIP
RELATIONSHIP
ATHENA (Download tool):
http://athena.ohdsi.org/
The basic query is to use the concept_relationship table for example to get
the RxNorm equivalent of a NDC code
SELECT ndc.concept_code, ndc.concept_id as source_concept_id,
ndc.concept_name, rxNorm.concept_id, rxNorm.concept_name
FROM concept ndc
JOIN concept_relationship r ON concept_id_1 = ndc.concept_id
JOIN concept rxnorm ON rxnorm.concept_id = concept_id_2
WHERE relationship_id = ‘Maps to’
and ndc.vocabulary_id = ‘NDC’ and ndc.source_code = ‘00719190213’
Is there a way we get the Crosswalk for
ICD9-ICD10-SNOMED
RxNrom-NDC
etc… etc
Basically I was looking for all the Patient table data to have a crosswalk… It would be great if we have it available via Athena…
This will give you crosswalk from ICD9/10 to SNOMED
CREATE OR REPLACE view source_to_concept_map_5
( source_vocabulary_id, source_concept_id, source_code, source_code_description, source_domain, source_standard_concept
, target_concept_id, target_vocabulary_id, target_concept_name, target_domain, target_standard_concept
)
AS
SELECT s.vocabulary_id AS source_vocabulary_id
, s.concept_id AS source_concept_id
, s.concept_code AS source_code
, s.concept_name AS source_code_description
, s.domain_id AS source_domain
, s.standard_concept AS source_standard_concept
, COALESCE(t.concept_id, 0 ) AS target_concept_id
, COALESCE(t.vocabulary_id, ‘None’ ) AS target_vocabulary_id
, COALESCE(t.concept_name, ‘No matching concept’ ) AS target_concept_name
, t.domain_id AS target_domain
, t.standard_concept AS target_standard_concept
FROM concept s
LEFT OUTER JOIN concept_relationship rel ON concept_id_1 = s.concept_id
AND relationship_id = ‘Maps to’
AND rel.invalid_reason IS NULL
LEFT OUTER JOIN concept t ON t.standard_concept = ‘S’ AND t.concept_id = concept_id_2
WHERE s.vocabulary_id IN( ‘ICD9CM’, ‘ICD10CM’ ) ;