I know that a user can create charts in the dashboard summary tab through selection of variants, patients, etc. I wanted to know if it is possible for a local instance of cBioPortal to add completely new charts based upon ad hoc user requests? For example, if a user of my local instance were to want to have a chart that shows a treatment visualization how would this be achieved?
My first thought is that the data would have to be provided as a custom data field in the “data_clinical_patient.txt” and/or “data_clinical_sample.txt” files and uploaded. The user could then manually add the desired chart in the summary dashboard tab using the “chart” button. Aside from this specific question, which I would like the answer on how to achieve, I also was also looking for clarity on how flexible the cBioPortal software is to other ad hoc user requests for visulizations? Can a developer add in new visualization methods to use within the portal dashboard(s)?
A second question, is related to the possibility of real-time data streaming to cBioPortal. Could a user populate their own database and have the data readable by cBioPortal and populate the studies/data in real-time from the currently active and maintained local database?
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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Good morning Ino,
Thank you so much for the thorough and extremely helpful information that you provided in your response email. I wanted to get clarification on the batch import you mentioned.
It is my understanding that cBioPortal does not allow for appending new data to a study that currently exists in an instance. In order to add new data, the import script is used to first remove the study then re-upload the study with the newest version of all of the corresponding files. Is my understanding of the workflow correct? If a user is using the batch import approach would they need to delete the existing studies or can adjustments be made to the import script to keep adding new data as it becomes available for the various studies that exist in a cBioPortal instance?
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Yes, this is very helpful. Our most likely use case is to add new patient data and not necessarily to append new pieces of data to existing patient samples records in the platform.
One additional question – how would cBioPortal handle a new table being added to the MySQL database on the backend? Could the platform handle a new table being referenced for a custom visualization for instance?
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