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ICD to snomed mapping

Implementers
#1

Hello,
Does concept relationship table on athena have the mapping for all icd9 and icd10 codes to SNOMED as per latest codes?
I could find some mismatch with respect to icd codes that I could find in my source data. So just wanted to confirm.

Thanks

#2

ICD10 mapping is the one that reviewed and fixed lately, so it has the best quality.

ICD10CM and ICD9CM mappings are relatively good, but require some improvement anyway.
So, they are reviewed now.
Please share your mismatch cases, so we can identify the problem.

#3

hi Rashmi,

Have you got your question answered? I am new to Athena mapping and involved in this because of our OMOP project.

I am very interested to find out the algorism and logic they use when applying ICD10 to SNOMED CT mapping, do you know who is the best person to contact? Thanks,

#4

Hi @LeileifromUK
Sorry, for the delayed reply.
First, we took couple of sources:

  • SNOMED refset “SNOMED to ICD10CM” mapping
  • UMLS provided equivalence.
    Both sources are about ICD10CM, but most of the common for ICD10 and ICD10CM concepts mean the same, so ICD10CM related sources were fine to start with.
    Some concepts had innacuttate mapping because of opposite direction (we need ICD10 to SNOMED, but sources gave SNOMED to ICD10). Some haven’t mapped at all.
  • used usagi ot get the match based on concept descriptions.
    Then, all these mappings were compared, and in some cases new relationships were generated by the OHDSI vocabulary team which mostly contains from medical professionals.
    So, the most important method in the creation of mapping is the manual curation by domain experts.
    Please let me know if you want to know further details.
#5

Sorry for bumping a old post over a dumb question.

So there exists a “suggested map” for ICD9 codes to OMOP? Where do I access that? Is it available in the current Athena downloads?

Thanks. If there is such a map, it would tremendously cut down our workload

Exporting ICD9CM mapping from Athena
#6

No problem, @lychenus

ICD9CM mapping is available in Athena. You can click on any ICD9CM concept and see relationship Non-standard to Standard map (OMOP). It is also available in downloads.

Check concept_relationship table for valid (invalid_reason IS NULL) relationship ‘Maps to’ and ‘Maps to value’ and you will find standard concepts ICD9CM is mapped to.

#7

Wow thanks.

Just interested if there is the same thing for IPCC and BNT codes?

It looks like there needs to be a special way to gain access to BNT for those outsidr Britain though. Thanks

#8

You mean the BNF, right?

IPCC and BNF are not added to the OMOP Vocabulary unfortunately.
You might try to search for links between dm+d and BNF since dm+d is fully adopted into OMOP and is also the UK drug registry.

Can you please share more information on IPCC? Maybe we can think together of some workarounds with it?

#9

ICD9CM mapping is available in Athena.

Hello, Thanks. Indeed it is. However I am slightly confused in the mapping.

My data is presented in the icd9 concept code. Like

162.3 Malignant neoplasm of upper lobe, bronchus or lung

Now from Athena I know that it is OMOP’ed to

261236 Primary malignant neoplasm of upper lobe, bronchus or lung

However, it does not show up ‘quite correctly’ in Usagi (where I downloaded the vocabulary list from Athena), because the data term is not exactly referred to the icd9 code (with some variations for example,).

162.3 Super bad Christmasss Trumor of upper lung

So is there anyway to download the whole list of icd9 map in the code form something like

162.3 → 261236

?

Thanks

#10

Yes, it is BNF. But I guess the BNF codes in my data is not exactly the best. It only states the type like

4.7.1,PARACETAMOL

It doesn’t really pinpoint anything. I guess I will leave it to Usagi (and boy it seems Usagi does quite a good job over that).

#11

I am sorry I am confused with all the terms (I really only have heard of icd9/10/11)

The correct term should be ICPC International Classification of Primary Care

I have all the codes, and I have to refer it to the internet lol. I have something like K86 which google says

ICPC-2 Code: K86 Hypertension uncomplicated
Source: RxReasoner

Seems like there isn’t a map from Athena though.

But Usagi still does a pretty good job thank god.

#12

Is it something you get after tranlating it? Since the description looks super weird.
Can you post the original name if it’s translated indeed

Yeah, it does a good job if there are simple terms like “Hypertension uncomplicated”.

#13

eh no lol. It was English. It is something I made up as the data wasn’t too supposed to be put onto the internet. But I think the clerk could be occasionally drunk there are some of those Xmas Trumor thing shows up.

And all I can believe is the icd9 code.

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#14

yeah, just stick with ICD9 code and its mapping

#15

yeah but hopefully there is a list something like 162.3 → 261236 otherwise there is still a lot to go through. haha

#16

Don’t worry, all ICD9 codes have mapping to SNOMED

#17

So taking any map to map ICD9 to SNOMED would mostly be OMOP’ed already? Sorry, there has been confusing information online.

#18

hi @lychenus, all existing ICD9CM codes (17564 items) have mappings to SNOMED in OMOP.

#19

To get this, load the downloaded vocabulary tables in a database and then use this source to standard SQL snippet:
sqlScripts.utf8, with source_vocabulary_id = 'ICD9CM'

Are you doing this work by any chance in the context of EHDEN? Then please reach out on the EHDEN forum with this question (https://forum.ehden.eu).

Also, I can highly recommend taking the EHDEN Academy on the OMOP CDM and on the OMOP vocabularies.

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Exporting ICD9CM mapping from Athena
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