icgc-argo / argo-dictionary

Development of the ARGO Data Dictionary
https://docs.icgc-argo.org/dictionary
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Update controlled terminology for anatomical_site_irradiated #315

Closed hknahal closed 2 years ago

hknahal commented 3 years ago

Update controlled terminology for anatomical_site_irradiated field in Radiation table, so it is in line with controlled terminology used by Cancer Care Ontario: https://ext.cancercare.on.ca/ext/databook/db2021/Appendix/Appendix_1.15_-_Body_Region_Codes_.htm The current controlled terminology used by Cancer Care Ontario has been updated to include more granularity. For example, the original controlled terminology used by Cancer Care Ontario was using the term "Thorax" and was missing the terms "Chest" which is applicable to Breast Cancer. The term "Extremities" has been split into "Lower Limb" and "Upper Limb". "Head-Neck" has been separated into two terms "Head" and "Neck". This is in keeping with the TCA Working Group's recommendation to keep this terminology very general (they did not recommend using ICD-O-3 codes for this field). This generalized list of terms can be mapped to mCODE's (SNOMED) terminology as well (RadiationTargetBodySiteVS)

Terms used in current CCO:

ABDOMEN BODY CHEST HEAD LOWER LIMB NECK PELVIS SKIN SPINE UPPER LIMB

Older CCO terminology: thorax (keep) brain (keep)

New List: ABDOMEN BODY BRAIN CHEST HEAD LIVER LOWER LIMB LUNG NECK PELVIS SKIN SPINE THORAX UPPER LIMB

akachru-github commented 3 years ago

Deployed and tested in QA

kcullion commented 2 years ago

Tested in Staging, and all of these values validate as expected:

Older CCO terminology:
thorax (keep)
brain (keep)

extremities (replaced by upper and lower limb)
bone (too general)
head-neck (split into head and neck)
liver (keep)
peritoneum (radiation is administered in abdomen area)
lung (keep)
kcullion commented 2 years ago

looks good in netlify docs site

hknahal commented 2 years ago

Added to dictionary version 1.13