Study example question

[Aaron Atkinson]

Hello group,

Some time ago I a cBioPortal study with separate outcomes data/file(s) from the patient clinical file(s).

If that memory is accurate any help in finding an example study that has separate outcomes from more static patient files would be appreciated.

In the alternative if I am just not seeing this option in the file format docs any help pointing that out would also be great.

Thanks, Aaron.

[Guizela Huelsz Prince]

Hi Aaron,

Are you maybe thinking about timeline files? These are files that contain longitudinal clinical events and are distinct from the primary data_clinical_patient.txt file. They are used to visualize events like treatment, surgery, and disease progression over time for individual patients. Here is an example of a patient view with timeline events: https://www.cbioportal.org/patient?studyId=lgg_ucsf_2014&caseId=P01

More info here: https://docs.cbioportal.org/file-formats/#timeline-data

Let me know if this helps.

Best,

Guizela

[Aaron Atkinson]

Thanks for your response Guizela,

I'm not talking about timeline files. Those are familiar and well documented as you noted. 

I'm talking about a cBioPortal study that had separate outcomes as in Overall survival and Progression free survival etc that were separate from the patient clinical data file. I thought I saw cBioPortal study that had outcomes separate in this way. My thought was to copy that so outcomes could be updated more readily.

Cheers, Aaron. 

[Guizela Huelsz Prince]

Hi Aaron,

I am not aware of any current functionality to handle two separate patient files. In fact, the metaImport script will produce an error if more than one file is marked as containing the PATIENT_ATTRIBUTES datatype.

A possible solution is to create a custom script that merges two patient data files before loading them into cBioPortal. When the survival data file is updated, you can run the script again and then use incremental loading. This option lets you include only the rows for patients whose data has changed, which speeds up the loading process since you don't need to reload the entire file.

If you can remember more details about the study you're referencing, such as the approximate date or cancer type, I can look into it further for you.

Best,
Guizela