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OHDSI / Vocabulary-v5.0

Build process for the OHDSI Standardized Vocabularies. Currently not available as independent release.
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Missing SNOMED Cancer Staging Concepts in OHDSI Vocabulary Distribution #837

Open mgurley opened 1 year ago

mgurley commented 1 year ago

Describe the problem in content There seem to be missing cancer staging concepts in the SNOMED ingestion into the OHDSI vocabulary distribution. AJCC, mCode, and SNOMED collaborated to represent cancer staging in SNOMED. See added SNOMED codes here:

http://build.fhir.org/ig/HL7/fhir-mCODE-ig/branches/master/ValueSet-mcode-tnm-primary-tumor-category-vs.html

How to find it If you search Athena for any of these added SNOMED codes, you will not find them. Example:

https://athena.ohdsi.org/search-terms/terms?vocabulary=SNOMED&page=1&pageSize=15&query=1228943009

Expected adjustments I think these concepts were added to the SNOMED international release dated 31-Jul 2022. But Athena lists the last update of SNOMED to be 27-Jan-2022. Are these concepts missing because SNOMED has not been refreshed since these concepts were added? Or is there another explanation? Can they be added?

Additional context We want to make maps from these SNOMED Staging concepts to the staging concepts in the Cancer Modifier vocabulary.

greenvet2 commented 1 year ago

In looking at the roadmap for Release planning that was recently released, the SNOMED refresh will happen with the Winter 2024 release.

aostropolets commented 1 year ago

@greenvet2 you looked at the roadmap! Love it! :) Michael, SNOMED will be released in winter. We are doing quite a big improvement of SNOMED processing to ensure that it is stable, reliable and clean. Will take some time. And SNOMED relationships are too complex to inject them manually.

Could you help me understand your use case better? You say that you want to map those to CM, which makes me think that you observed a data source using those SNOMED codes to code stages. Is that correct? Or can your source data be mapped to CM directly?

mgurley commented 1 year ago

@aostropolets Since mCode is proposing to collect cancer staging variables mapped to these SNOMED codes, and since mCode standardizes how data is collected and mapped at the point of care in EHRs, it will be important for these codes to be present as non-standard source concepts that are mapped to the appropriate standard concepts in the Cancer Modifier vocabulary. Because source data will be coded in these SNOMED codes.

Also, beyond wanting to have these concepts in OHDSI to be able to map them to the Cancer Modifier vocabulary, I think it's reasonable expectation that ALL SNOMED codes in recent (greater than 6 months) SNOMED distributions are present in the OHDSI distribution. Like I mentioned, these were introduced into SNOMED about a year ago. Sorry if this is documented elsewhere, but which version of SNOMED is ingested into OHDSI, the International or the US version?

So, just to confirm:

aostropolets commented 1 year ago
  1. I don't see why they wouldn't. We should double-check closer to release date of course.
  2. That would fall into modification of content category (de-stadardization is basically deprecating Maps to to itself + creating new mappings to Cancer Modifier). Modification means there will be review involved - review of Vocabulary Team and Oncology WG, so additional iterations may be required. I would suggest opening a new issue under "Modification of content" category, describing in some detail the proposed mappings with the examples (examples can be in plain text or in the form of template 6 modifying mappings) and we will go together from there.