Versioning of OncoKB

[kpjonsson]

Is there any way to use specific versions of OncoKB itself (not the annotator)?

Say for example I wanted to stick to the release from May 9, 2019 here: https://oncokb.org/news.

[zhx828]

@kpjonsson we currently don't have anything set up for that. If you want, you could set up your own oncokb instance, the sql dump is here https://github.com/oncokb/oncokb-public/tree/master/data/v1.20

@jjgao do you think setting up previous versions should be supported?

[kpjonsson]

Thanks @zhx828.

[jjgao]

@zhx828 maybe we can provide docker files in the future for that... but probably not a priority.

[evanbiederstedt]

I do think this may one day become more of a priority (though not soon). I'm happy to help out .

Please send over some marching orders

maybe we can provide docker files in the future for that... but probably not a priority.

I'm happy to help out building Docker images.

EDIT: I took a closer look into this. Yes, it's not a majority priority any time soon.

[zhx828]

@evanbiederstedt thanks for looking into the issue. We actually using docker to do production release. Just need to create few more for previous versions. I do think this is something nice to do and not really difficult. But where should we host these instances? Or should we just let the users host their own by using the docker image? @jjgao thoughts?

[evanbiederstedt]

I do think this is something nice to do and not really difficult. But where should we host these instances? Or should we just let the users host their own by using the docker image?

I'll slack. I would recommend hosting the Docker images (with organized version schema) on Dockerhub, e.g. this domain would be good https://hub.docker.com/u/onkokb

You can set it up to host the Dockerfiles on Dockerhub, but I think it makes more sense to host them at this repo: e.g.

oncokb/oncokb-annotator/subDirectoryName/Dockerfile

Users can then build the Docker image from that file.

(Caveat: everything I say can be dismissed as unhelpful recommendations.)

[tingchiafelix]

Hi,
I'm also looking for a way to lock down the oncoKB version. Could I know if you have any updates on this topic?

Thank you in advance,
TC

[zhx828]

@tingchiafelix we haven't made any progress yet, a bit short on the resource to do that. But could you give us more information on how you like to use the versioned oncokb content? Do you prefer to annotate by sending the version, or use a dedicated url?

[tingchiafelix]

@zhx828 thanks for your response. Actually, I have an API token obtained from the oncoKB license team and I didn't see any option to specify a version by running API annotator. In our research, we hope to lock down certain versions of OncoKB for annotation. Do you have any suggestions on that?

Also, another naive question. When I do the OncoKB annotation via API annotator, I assume the results are from the latest version of oncoKB database. Is that correct?

[zhx828]

@tingchiafelix correct, it uses the latest content from OncoKB and can generate a README file to include the data version info etc. Please see https://github.com/oncokb/oncokb-annotator/blob/master/example.sh#L44

We do not support versioned OncoKB content yet but that's definitely on our road map. We will keep you posted when that becomes available.