Citing data from GDC portal

Question

[noorpratap.singh]

Hi, I know this might sound stupid and I would like to apologise but I was wondering how exactly to cite data downloaded from GDC portal. I know usually people cite TCGA papers for individual cancer project but they now belong to legacy archive and since now data has been updated with more samples being added for almost all cancers. How to cite data for particular cancer? Also would it vary depending on the type of data we want to cite(SNP or expression)?

[GenoMax]

Your questions are partially answered by GDC FAQ. You may want to contact GDC support for specific questions.

Answer 1

[roy.granit]

This is what the GDC site says:

"Please credit the NCI Genomic Data Commons (GDC) in your manuscript by citing the following paper about the GDC in your manuscript:

Grossman, Robert L., Heath, Allison P., Ferretti, Vincent, Varmus, Harold E., Lowy, Douglas R., Kibbe, Warren A., Staudt, Louis M. (2016) Toward a Shared Vision for Cancer Genomic Data. New England Journal of Medicine375:12, 1109-1112

When citing individual projects, please refer to the attribution policies of the project when available."

So I guess that if you are using the "provisional" data that is added after a specific study was published you should cite the MS mentioned above.

[noorpratap.singh]

I had read the FAQ and the source you site above. I am though still not clear with the following: "When citing individual projects, please refer to the attribution policies of the project when available." I know I have to cite the above manuscript but what about the actual data source and how to retrieve information about that.