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Add grade to disease object #38

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pnrobinson opened this issue Nov 28, 2023 · 1 comment
Open

Add grade to disease object #38

pnrobinson opened this issue Nov 28, 2023 · 1 comment

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@pnrobinson
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The diagnosis table includes information about grade, e.g. G3.

In the GA4GH Phenopacket Schema, there is a field "tumor_grade". Usually, grade refers to the histological appearance of tumor cells and so this field seems to fit better in "biospecimen" rather than "diagnosis".

To do, clarify the intended meaning of this field and enter the information. accordingly.

@msierk
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msierk commented Dec 12, 2023

I don’t know if this is useful to us, but this notebook has some examples converting GDC data to the CCDH data model. It does say that in their model (the CCDH model) specimens are associated with diagnoses rather than with Research Subjects. But there still might be some useful examples here. See the create_stage_from_gdc function.

https://github.com/cancerDHC/example-data/blob/main/GDC%20to%20CCDH%20conversion.ipynb

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