Ensuring TCGA Acronyms are in Oncotree

[Augustin Luna]

It was really nice that Oncotree has the UMLS categories and wanted to extract them the for TCGA acronyms. I found out some of the TCGA acronyms are not present:

"DLBC" "KIRC" "LAML" "LGG"  "LIHC" "MESO" "OV" "THCA"

I think the TCGA acronyms (and data) and still widely used. Searching for DLBC, KIRC, THCA, etc brings up the appropriate study on cBioPortal, but no results in Oncotree.

I'm going to assume the Oncotree developers were aware of the TCGA acronyms and did not include them for some specific reason. Could these be added in a way that does not disrupt ongoing activities? Perhaps add the all the TCGA acronyms to "history" or "externalReferences" in the data underlying Oncotree even if now things have evolved.

Thanks,
Augustin Luna

[Nikolaus Schultz]

Hi Augustin,

This is a good point. We deliberately created new codes for certain tumor types (e.g., “OV" for high grade serous ovarian cancer was simply not specific enough, or “AML” was a more intuitive label than “LAML"), but we can consider adding a mapping for the missing ones. 

Niki.

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