Local cBioPortal instance - data question

[Joseph, Greg]

Hello,

 

It is my understanding that the traditional dataflow for cBioPortal is that a study is uploaded once, and that the dataset for the study is assumed to be complete and final, with no new data expected. This is based on cBioPortal pulling data that is connected to a publication and that any new data or analysis would appear as a separate and unique publication. Is cBioPortal capable of handling the addition of new data to an existing study within a local cBioPortal instance?

 

I assume that if new data were to become available for an existing study, the developer/maintainer of the local database would have to use the MetaImport script to remove the existing study, then upload the study again with the newest versions of all required files. Is my understanding correct and is there a recommended workflow to follow for updating existing studies with new data?

 

Thank you,

Greg Joseph

 

Gregory Joseph, MS

Research Informatics Analyst

Winship DATA Shared Resource

Winship Cancer Institute at Emory University

1814 Clairmont Road

Decatur, GA 30033

 

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[Benjamin Gross]

Hi Greg,

Your understanding is correct.  Currently, we have no way to update an existing study.  The correct workflow would be to remove and then import with the updated data files.

Best,

Benjamin

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[Ekaterina Vansovich]

Hey all,

I'd like to ask if there are any updates on it. Is there a way to update an existing study? This feature would be very handful :)

Best Regards
Ekaterina 

[Benjamin Gross]

Hi Ekaterina,

Unfortunately, we have not had a chance to provide this behavior.

Best,

-Benjamin

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[Ji Hen Lau]

Hi all,

I have two related questions:

1. Would there be plan on supporting the update to existing studies?  
2. If the samples that have been analyzed across different analyses (same clinical samples but different molecular analyses), is there a way to just import the new analysis? Or similarly, the only way to do so is delete and re-import the whole study with the new analysis data.

Thank you for your help!

Best regards,
Ji Hen

[Priti Kumari]

Hi Ji Hen,

The feature for incremental data loading has been released: https://github.com/cBioPortal/cbioportal/releases?q=incremental&expanded=true
Feel free to reach out if you have further questions.

Best,

Priti

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[Ji Hen Lau]

Hi Pitri,

Thanks for the reply! I will try it out and get back to you if I face any issue !

Regards,

Ji Hen

[Pieter Lukasse]

Hi Ji Hen,

How did this go?

Best,

Pieter

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