Question: TCGA/GDC data portal. Clinical features description
1
gravatar for rbrtdambrosio
2.2 years ago by
rbrtdambrosio60 wrote:

Hello,

I'm using the TCGA/GDC data related to Colon Adenocarcinoma (COAD) I have retrieved the data from Firebrowse: http://firebrowse.org/?cohort=COAD# that allows a simply access to the data.

I downloaded the clinical data: gdac.broadinstitute.org_COAD.Merge_Clinical.Level_1.2016012800.0.0/

and I'm using the file COAD.merged_only_clinical_clin_format.txt

that contains the clinical feature of each patient.

My problem is that I can't find anywhere the description of those clinical features. Ad examples there are:

  • patient.follow_ups.follow_up.new_tumor_events.new_tumor_event.days_to_new_tumor_event_after_initial_treatment
  • patient.new_tumor_events.new_tumor_event.days_to_new_tumor_event_after_initial_treatment

From the name is not easy to understand exactly which is the difference of this features. And the same happens for other features.

I gave a look to https://cdebrowser.nci.nih.gov/CDEBrowser/ but the amount of information is very limited.

Where can I find additional information about these clinical information?

Thanks

clinical gdc tcga R firebrowse • 2.4k views
ADD COMMENTlink modified 15 months ago by bioInfo0 • written 2.2 years ago by rbrtdambrosio60
1

The information you wanted was stored in tcga-data.nci.nih.gov/docs/dictionary/TCGA_BCR_DataDictionary.xml but it was recently removed. For the GDC data model the description can be found here: https://gdc.nci.nih.gov/about-data/data-harmonization-and-generation/clinical-data-harmonization. However, those fields are not listed.

Maybe sending and email to TCGA or GDC support might help you.

ADD REPLYlink written 2.2 years ago by tiagochst70
0
gravatar for bioInfo
15 months ago by
bioInfo0
bioInfo0 wrote:

Hi, is there still a solution?

ADD COMMENTlink written 15 months ago by bioInfo0
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