Expected vocabulary changes during February 2025 release

Vocabulary Users
1

Dear all,

In this topic, the Vocabulary team will share the expected changes in the OHDSI vocabularies during the upcoming Feb 2025 release.

During this release, we expect some major changes previously discussed in the Community:

  • Rollback of CPT4/HCPCS mapping to the Visit domain (discussed here)
  • Rollback of SNOMED evaluation finding post-coordination and revision of pre-coordinated measurement domains both in SNOMED and in the source vocabularies (discussed here)

These changes are expected to affect the ETL and cohorts significantly, and we encourage users to review the files provided here and assess the potential impact.

I have attached the Excel files containing SNOMED changes in concept standard status, domains, and mapping in this post. Please, feel free to explore them and report any issues you have.

SNOMED concept changes.xlsx (310.4 KB)
SNOMED mapping changes.xlsx (435.7 KB)

2 Likes
2

Dear all,

Here I attach Excel files containing expected changes in CPT4 and HCPCS concepts and their mapping. During this release:

  • We deprecate mappings to visits and make the source CPT4 and HCPCS concepts standard Procedures and Observations.
  • Instead, we introduce a new relationship ‘Has associated visit’ that now links CPT4 and HCPCS concepts with the Visit domain.

Please, feel free to explore.

CPT4 concept changes.xlsx (69.2 KB)
CPT4 mapping changes.xlsx (84.9 KB)
HCPCS concept changes.xlsx (45.6 KB)
HCPCS mapping changes.xlsx (31.3 KB)

3

Masha, this SNOMED mapping changes are helpful, but maybe it’s worth to share the source concepts (ICD mostly) mapping changes as well? So the users can see how their data mapping is changed?

4

Hi Dima,
Sure, I will share source vocabularies’ mapping changes as well, as soon as we finish our work on them.

1 Like
5

Hi all!

Here I attach Excel files with mapping changes for ICD vocabularies. You can find the following fields there:

  • source_concept_id, source_standard_concept, concept_name - attributes of source concepts
  • old_relationship_id_agg, old_target_concept_id_agg, old_target_concept_name_agg - mappings currently present in Athena
  • new_relationship_id_agg, new_target_concept_id_agg, new_target_concept_name_agg - mappings that are expected in Feb 2025 release

Please, feel free to explore them and report any problems you have.

Best,
Masha

ICD9CM_mapping_changes.xlsx (48.0 KB)
ICD10_mapping_changes.xlsx (58.2 KB)
ICD10CM_mapping_changes.xlsx (223.8 KB)
ICD10CN_mapping_changes.xlsx (91.9 KB)
ICD10GM_mapping_changes.xlsx (62.1 KB)
CIM10_mapping_changes.xlsx (63.2 KB)
KCD7_mapping_changes.xlsx (60.0 KB)

6

HI all, We are a bit new to understanding the vocabulary updating process both for OHDSI and our local instance. I could not find a clear answer on the website to:

  1. What is the release cycle for vocabularies? I’ve seen quarterly mentioned as a target but it look like the last update was August.
  2. We are finding that some quite a few RxNorm codes in our data that is not in the current vocabulary in athena. RxNorm is apparently released on a monthly basis but the current version in Athena is from May 2024.

I fully understand and ppreciate that this is a bunch of work so not critquiing, but just trying to understand release cycles and how people deal with codes that are not yet in the standard vocabs.

Thanks!

Rob

7

Hi, Rob!

OHDSI vocabulary releases take place twice a year: in February and in August. Since preparing the vocabulary for release takes some time, the source version usually lags behind the release date, although the Vocabulary team always tries to release as new a version as possible.

On our GitHub repository you can find the roadmap with the planned scope of the nearest releases and anticipated versions of source vocabularies to be released.

Best, Masha

8

Hi Masha,
We recently updated our vocabulary at UTSW, and it appears that previously mapped standard concepts for smoking statuses have now been reclassified as non-standard. The new standard concepts belong to the OMOP Extension vocabulary and seem to offer more specificity. For example, the source code “Light Tobacco Smoker” was previously mapped to concept ID 762498, which now shows as non-standard. Could you please provide more details about these changes?

9

Hello!

In 2023 we introduced a new hierarchy of smoking, you can find the details here. The changes you describe are related to the implemented hierarchy.