Data upload from novel data from published work in Nature or other journals

[Lal, Samir]

To Whom It May Concern,

 

If we publish genomic data (Whole exome-seq and RNA-seq) in a Nature Communications paper or another Nature paper and would like to make our data available as part for the cBioportal platform what are the procedures involved?

 

Is there any cost involved?

 

What if we have little experience with databases?

 

Also If our manuscript is in review/ or is accepted pending minor changes can we delay the date of release?

 

I hope you can help me understand how this can be accomplished.

 

Kind Regards,

 

Samir Lal

Postdoctoral Fellow

[JJ Gao]

Hi Samir,

I just noticed you also emailed this list with more details. Please disregard my previous response. Let's use this thread here.

First of all, thank you for your interest in depositing data into cBioPortal!

For your questions: 

> Is there any cost involved?

There will be no cost for depositing published datasets. 

> What if we have little experience with databases?

You don't need database experience. It would be great if you can prepare your data in the right format (https://cbioportal.readthedocs.io/en/latest/File-Formats.html). There are example data files on our datahub (https://github.com/cBioPortal/datahub/). 

> Also If our manuscript is in review/ or is accepted pending minor changes can we delay the date of release?

I would recommend releasing the data after the publication.

To proceed, here are the data files we will need:

• MAF
  
• Copy number alterations (do you call copy number data from the WES data?):  continuous gene level data (e.g. log2), discrete gene-level data (e.g. gistic), and segment file.
  
• Expression matrix (gene vs samples)
  

Could you also create an issue per dataset/publication on https://github.com/cBioPortal/datahub/issues/new? Our data curator can then help in the process.

Please feel free to let us know if you have any questions.

Best,

-JJ

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