cancer type study

[Alain Pacis]

Hello,

I've downloaded this data from cBioPortal as a test data:

https://www.cbioportal.org/study/summary?id=breast_cptac_gdc

I tried uploading it on cBioPortal docker and received one error: "Cancer type of study is neither known to the portal nor defined in a cancer_type file" (see below).

I also tried using brca or BRCA in the parameter type_of_cancer in meta_study.txt .

Could you please with this issue?

Thank you,

Alain

Alain Pacis, PhD

Bioinformatics Specialist
Canadian Centre for Computational Genomics
Rosalind and Morris Goodman Cancer Institute

https://computationalgenomics.ca/services/

[Prasanna Jagannathan]

Hi Alain

Thanks for the email. Is the database setup properly and the sample study is working well including running queries? Usually the error message indicates that the seed database was not properly installed.

In the cBioPortal database, "type_of_cancer" table has all the cancer types that can be imported. If possible, check if the table has the right cancer types that you want to import.

Please reply only to the cBioPortal group.

thanks

Jag

--
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/cbioportal/YT3PR01MB87068E367A658C2C5F64AB0BFB1CA%40YT3PR01MB8706.CANPRD01.PROD.OUTLOOK.COM.

[Alain Pacis]

Thank you for your reply.

Could you please point me to this "type_of_cancer" table? Or please provide the list in this email.

"In the cBioPortal database, "type_of_cancer" table has all the cancer types that can be imported."

Thanks,

Alain

---

From: Prasanna Jagannathan <jagn...@gmail.com>
Sent: September 26, 2025 11:26 AM
To: Alain Pacis <alain...@mcgill.ca>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>; David Lougheed, Mr <david.l...@mcgill.ca>
Subject: Re: [cbioportal] cancer type study

 

You don't often get email from jagn...@gmail.com. Learn why this is important