Labels for cancer subtyping
JackyC666 opened this issue · comments
Hi, How did you label the BRCA dataset? In your paper,
TCGA-BRCA includes two sub-types of cancers, Inva-
sive Ductal Carcinoma (IDC) and Invasive Lobular Carci-
noma (ILC). There are 779 IDC slides and 198 ILC slides.
So, HOW can I REPEAT it?
In the TCGA DATASET,I can`t found something about it!
Thanks~~
I got these labels from the clinical.json
file obtained from the GDC
website, specifically:
- I first downloaded the
clinical.json
file underDiagnostic Slide
ofTCGA-BRCA
project from the GDC official website. - Second, I obtained the
case_id
andprimary_diagnosis
fields for each case from that file. - Finally, I classified the
primary_diagnosis
field containing the IDC or ILC subtype keyword as either IDC or ILC. Thus, I got the BRCA labels that I am using now.
Since I haven't found any other way to process this either, I'm not sure if this is entirely appropriate, so if you have a better idea, feel free to leave a comment.
I got these labels from the
clinical.json
file obtained from theGDC
website, specifically:
- I first downloaded the
clinical.json
file underDiagnostic Slide
ofTCGA-BRCA
project from the GDC official website.- Second, I obtained the
case_id
andprimary_diagnosis
fields for each case from that file.- Finally, I classified the
primary_diagnosis
field containing the IDC or ILC subtype keyword as either IDC or ILC. Thus, I got the BRCA labels that I am using now.Since I haven't found any other way to process this either, I'm not sure if this is entirely appropriate, so if you have a better idea, feel free to leave a comment.
Thanks for your reply!
where is the primary_diagnosis
?
Can you give me a link?
Or a screenshot to illustrate?
Sincerely thank you for your help!