Missing SNOMED to ICD mapping

Vocabulary Users
1

Noiced that some SNOMED to ICD mapping are missing from the download of vocabularies.
Here are some examples:

Missing ICD code:

SOURCE: SNOMED - CONCEPT_CODE: 102447009 CONCEPT_ID: 4010333 (Postmenopausal osteoporosis)

  • When compared in athena.ohdsi.org - I see ICD10 codes such as concept_code: M81.0 (concept_id: 45538882)

But I do not see this ICD10 code in the downloaded concepts.

Am I missing anything or else is there an issue with concepts that I have downloaded (a month ago) ?

Here is the query that I was running:

WITH CTE_VOCAB_MAP AS (
select conc1.vocabulary_id as SOURCE_VOCABULARY_ID, conc1.concept_id as SOURCE_CONCEPT_ID, conc1.concept_code as SOURCE_CONCEPT_CODE, conc2.vocabulary_id as TARGET_VOCABULARY_ID, conc2.concept_id as TARGET_CONCEPT_ID, conc2.concept_code as TARGET_CONCEPT_CODE
from concept conc1
inner join concept_relationship crel
on conc1.concept_id = crel.concept_id_1 and crel.relationship_id = ‘Mapped from’
inner JOIN concept conc2
ON crel.concept_id_2 = conc2.concept_id
)
SELECT *
FROM CTE_VOCAB_MAP
WHERE SOURCE_VOCABULARY_ID IN (‘SNOMED’)
and source_concept_code = ‘102447009’

2

well, one of the rows your script returns is:

SNOMED | 4010333 | 102447009 | ICD10 | 45538882 | M81.0

Did you check the checkbox for ICD10 and SNOMED before download the vocabularies?

3

I did download SNOMED and ICD10. Some of the other codes are coming through… ie.,
for SNOMED - 20433007 - my query returns ICD10CM - S89.04

Which confirms that in the download that I got I have relations between SNOMED TO ICD10. It appears some of the data is missing in the download that I got.

So it looks like the source - ohdsi athena files has the information. Let me re-download and re-load the concepts.

Btw… I am loading all this data using hadoop/impala scripts. Not sure if there is anything funny going on in those scripts.

Will re-load the data and will ping you back. Thanks for responding. Appreciate you looking into the issue.

4

I downloaded concepts again from Athena and re-loaded them. I am now able to see the missing SNOMED to ICD10 mappings. @Dymshyts - Thank you for looking into it. Appreciate the help.

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