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Read CTV3 vocabulary

Vocabulary Users
#1

CTV3 (Read v3) appears missing from Athena and elsewhere as a defined vocabulary for use with the OMOP CDM. I see Read listed, but this appears to be Read v2.

I’d appreciate any help locating the CTV3 vocab. or confirmation that CTV3 is not available or might be somehow merged with Read v2, or ?

https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:vocabulary

Thanks,
John

#2

@mysakjs:

Hm. We are actually waiting for Read to go away entirely. The NHS has mandated SNOMED. Read itself is frozen at this time, and no new codes are issued. For some reasons, the EHR vendors have not yet swapped. SNOMED has CTV3 in it, and we incorporate SNOMED UK into the overall SNOMED release.

Is there any reason you need specifically CTV3?

#3

If snomed ct has support for CTV3 we may be ok without having to map manually. Just trying to gauge whether we can use an existing vocabulary or whether we’ll need to build up our own using the SOURCE_TO_CONCEPT_MAP table or otherwise. CTV3 support (or manually mapping) is necessary for us to deal with EHR records that have not yet swapped but yea it’s mandated by the NHS as you say and all will presumably cut over eventually. I noticed there’s a vocab for Read v2, but was hunting for a comparable vocabulary for CTV3/ Read v3, if one existed. I’ll have a look at the snomed ct vocab and how ctv3 is represented therein. Appreciate the help.

#4

@mysakjs:

Well, it probably makes little sense to bring CTV3 into the Standardized Vocabularies as its life expectancy is short. However, the NHS provides mapping tables here.

To make it easy for you I extracted the CTV3 to SNOMED mapping. Please download from the OHDSI FTP site ftp://ftp.ohdsi.org. In the CTV3 folder there is the file CTV3_to_Snomed_MAP.xlsx. It has 4 fields:

  • CTV3_SCUI: One of the CTV3 identifiers
  • CTV3_STUI: Another CTV3 identifier
  • SNOMED_CODE:
  • ASSURED: They are providing a one to many mapping. One of the many is “assured”. At least, that’s what it looks like. There is no explicit documentation, or at least I cannot find it.

You may want to convert that thing into a proper SOURCE_TO_CONCEPT_MAP table. You need to pick which of the identifiers you need to use, and convert the SNOMED code into OMOP concept_id.

What kind of data are you working with that has CTV3?

#5

Working with UK patient EHR/GP data. Appreciate the confirmation to use source_to_concept_map table. This was my original/main question if we needed to map manually, and yea we have the mapping details from NHS- thanks much. Just wanted to make sure i wasn’t missing the CTV3 vocab, since I found Read v2 but not v3. Understand it doesn’t make sense to add at this point given the short life expectancy as you say, thanks.

John

#6

@Christian_Reich – can you share this file once more? We may need it for UK Biobank usage.

#7

Placed it in Teams.

1 Like
#8

Thanks, got it!

#9

@Christian_Reich @Ajit_Londhe
Can someone please share CTV3_to_Snomed_MAP.xlsx file again, I need it for UKbiobank related work. Your help is much appreciated.

#10

@mik Are there any plans to add CTV3 as a source vocab to the OMOP vocabularies?

The NHS already provides crosslinks between CTV3, READv2 and SNOMED with this TRUD resource. One of the challenges is the aforementioned one-to-many mappings they provide. But this can be easily tackled by e.g. only taking the preferred term.

I would say it is a relatively easy win.

#11

hi @MaximMoinat , I understand there is still some historic data around that would use Read CTv3. As outlined above, the use case would have to be strong to justify the effort (it is not something that would require mapping from scratch, but it will still be considerable effort to process it). We will however take it into consideration and will see if we can make it happen.

#12

Thanks Mik! Let me know if anything will be moving on this front, would be happy to help out.

t