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OHDSI / OncologyWG

Oncology Working Group Repository
https://ohdsi.github.io/OncologyWG
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ICD-O vocabulary issues #240

Closed sratwani closed 2 years ago

sratwani commented 4 years ago

Issue #1 - Topography w/o any conditions linked Issue #2 - ICDO Topogrpahy linked via 'Has Histology ICDO' to another Topography Issue #3 - ICDO Topography not mapped to SNOMED (89 out of 400) Issue #4 - Topography concepts without parent concept (315 out of 400) Queries are in the below spreadsheet. ICD-O Issues 2019-12-22.xlsx

sratwani commented 4 years ago

@ekorchmar has completed the documentation for mapping of ICDO to SNOMED for @cgreich and @rimusia review.

sratwani commented 4 years ago

@ekorchmar Is it okay to mark this as closed?

ekorchmar commented 4 years ago

We had a short call with @cgreich today and discussed all remaining issues. Yes, it should be closed.

sratwani commented 4 years ago

@ekorchmar so the changes are released?

sratwani commented 4 years ago

Documentation is complete. Changes to vocabulary are still pending.

sratwani commented 4 years ago

Per call on 1/6/2020, ICDO vocabulary issues have been documented. We standardize ICDO to SNOMED. Overall quality will be much better after SNOMED 3.2 release which is scheduled for April after which the plan is to release the fixes to the ICDO vocabulary issues.

ekorchmar commented 4 years ago

In our recent correspondence with SNOMED team it was confirmed that ICDO3.2 is expected to be a part of July 2020 release, which unfortunately means that it will be ready for inclusion in OMOP CDM only around October.

rimusia commented 4 years ago

Issues ##1, 2, and 4 are not related to SNOMED mappings and need to be fixed now. Please let the team know when to expect these fixes.

We detected one more issue #5 that looks quite serious: duplicate concepts, one of each should be deprecated. There are 495 such duplicates: select count() from ( select count() as total from concept where vocabulary_id = 'ICDO3' group by concept_name having count(*) > 1 ) a

An example below includes a reference to SEER which states that 9754/3-C02.9 is deprecated and 9751/3-C02.9 should be used instead:

1. 36554961 | 9754/3-C02.9 | Langerhans cell histiocytosis, disseminated of tongue, NOS | ICDO Condition | Standard | Valid | Condition | ICDO3

https://seer.cancer.gov/seertools/hemelymph/51f6cf5ae3e27c3994bd54b6/

2. 36567447 | 9751/3-C02.9 | Langerhans cell histiocytosis, disseminated of tongue, NOS | ICDO Condition | Standard | Valid | Condition | ICDO3

ekorchmar commented 4 years ago

I described the ongoning process of ICDO3 fixes on the wiki article:

Reported issues are caused by problems described in the article.

  1. Is actually related to classification level of topography that is never encountered in user data. It's problem number 4 in Wiki article.
  2. These relations were built by mistake long time ago. They are invalid.
  3. Being adressed by fixing problems 2 and 4 of wiki article
  4. Again, problem number 4
mgurley commented 2 years ago

Closing and placing in the deep backlog to focus the repository.