Reference Genome

[elias]

Hello, my name is Elias. 

I'm currently trying to figure out wich set of Genes Entrez_ID and Hugo Symbol cBioPortal is using with the docker setup? And if maybe there is a way to change this without the need to remove all Studies from our cBioPortal instance. 

Thanks for your Help! 

Best regards,

Elias

[Tim Kuijpers]

Dear Elias,

Thank you for reaching out! You can quite easily get the list of genes (Hugo Symbol, Entrez Gene ID, and type) by using the /api/genes endpoint.  This endpoint can be called with a curl command:

curl -X 'GET' 'https://<host-url>/api/genes projection=SUMMARY&pageSize=10&pageNumber=0&direction=ASC' -H 'accept: application/json'

Note that you have to change the <host-url> to your actual host, and add an offline token when you are running cBioPortal with Keycloak enabled.

I believe the documentation does explain the process to update genes and gene aliases step-by-step:  Updating gene and gene alias. 

I  hope this helps! If you have any further questions, please hit reply all, so our continued conversation is captured by the cBioPortal Google groups.

Best,

Tim

[Tim Kuijpers]

Dear Elias,

For some reason your second question did not end up in the board (and only in my inbox). I've copied it below since it might help others as well:

Hello Tim,

Thanks for your answer! I just have another question. Is it specified what the source of this gene list is? We are currently trying to figure out if we need to change this, so knowing which Database the genes are used from would be quite Helpful as well as finding out the Version we have in our Database at the Moment.

Best regards,

Elias

The source of this gene list can be found here: https://github.com/cBioPortal/datahub/blob/master/seedDB/README.md . Each database version contains a link to the HGNC release.

I  hope this helps! If you have any further questions, please hit reply all, so our continued conversation is captured by the cBioPortal Google groups

Best,

Tim