search

ncihtan / data-models

Schema.org Data Models for HTAN
MIT License
14 stars 6 forks source link

Update permissible values to v5 of ICD-O codes for Clinical Tier 1 Diagnosis Morphology and Primary Diagnosis #356

Closed kristenanton closed 1 month ago

kristenanton commented 4 months ago

Proposed change:

Update the permissible values for the Morphology and Primary Diagnosis data elements in Clinical Tier 1 Diagnosis to version 5 of ICD-O codes from version 3 (current, according to Morphology description).

ICD-O version 5 has included values that describe precancerous lesions, e.g., Atypical adenomatous hyperplasia (8250/0) and Minimally invasive adenocarcinomas, mucinous (8257/3). Allowing precancer atlases to provide this data will facilitate our identification of precancer cases in the HTAN dataset.

Per discussion in HTAN DCC Operations meeting:

Kristen will

  1. Look into the current permissible value lists (are they a subset of the ICD-O v3 codes?)
  2. Define a subset of the new coding that could be included in the current permissible value lists to meet the need
  3. Recommend updates to the descriptions of the data elements for accuracy
  4. Suggest a longer-term plan for updating the ICD-O based data elements (including having coding and corresponding text terms linked)

  5. How important is this feature?

    • 🌗 Medium - can do work without it; but it's important (e.g. to save time or for convenience) Kristen will work on this as a high priority, of medium urgency for implementation
kristenanton commented 4 months ago

All, I am looking more closely into this issue and it looks like the full WHO ICD-O is actually version 3.2 (released 2019), however the WHO 'Classification of Tumours' is version 5 (2021) ... requiring me to look into this more closely to figure out what is what. I'll update asap!

aclayton555 commented 2 months ago

As it relates to morphology codes, might also be helpful to cross-reference the context from this ticket: https://github.com/ncihtan/data-models/issues/334

adamjtaylor commented 1 month ago

Discussed with @kristenanton in HTAN Ops (?) meeting that we will just implement a regex for ICD-0-3 style codes - 4 digits followed by / followed by a single integer in range 0-3

adamjtaylor commented 1 month ago

Closing as was implemented in #407