Multiomics - Server Question

[sstemann]

We're trying to document our federated dev environment, I can't seem to get the server info from SmartAPI, could you take a look at the table here:

https://github.com/NCATSTranslator/TranslatorPM/blob/main/Translator%20Server%20Info.md

And either update directly in the markdown or update this ticket. We have the following KPs for your team:

• Wellness Provider
• BigGim
• Drug Response Provider
• TCGA Mutation Frequency Provider
• Clinical Risk Provider
• BigQuery Table

@NCATSTranslator/multiomics-provider sorry to tag the whole team but I'm not sure who to work with to get these updates! Thanks for your help!

[rtroper]

Okay, I've created a pull request to add the server for our KPs that are hosted on the service provider server: #67

[sstemann]

@rtroper thank you! for the goal to have a hosted Dev environment - will any of the Multiomics KPs be hosted by NCATS or do you prefer to engage in an SLA?

[sstemann]

@rtroper just following up on the comment above and adding one more question - is Big Query Table a KP? thanks!

[rtroper]

@rtroper just following up on the comment above and adding one more question - is Big Query Table a KP? thanks!

Sarah - We do not plan to have any KPs hosted in BigQuery. There's a chance that, for at least one KP, we'll store the data for the KP in a BigQuery table and then use a parser in combination with the Service Provider group's Biothings Studio tool to load (or update) the KP hosted on their server. Our plan right now is to keep all our KPs on their server (biothings.ncats.io).

[rtroper]

@rtroper thank you! for the goal to have a hosted Dev environment - will any of the Multiomics KPs be hosted by NCATS or do you prefer to engage in an SLA?

I apologize I haven't responded to this yet. Let me get back to you shortly.

[sstemann]

thanks!

[kevinxin90]

Hi @sstemann , so currently all KPs from Multiomics Provider are hosted by Service Provider at biothings.ncats.io. This is an AWS instance assigned to the Service Provider by NCATS. Does that count as "hosted by NCATS". Or do we still need a SLA?

[sstemann]

thank you for bringing this up - so I know Ryan's been saying this but i didn't click for me. So, when there's a new version of a multiomics KP, you push it to the biothings instance?

[kevinxin90]

Yes. That's right. There's a semi-automated pipeline to go from a KGX file to an API served at the biothings instance.

[sstemann]

Seems okay to me, I know currently Biothings is hosted by an NCATS Cloud instance, but this is not an NCATS ITRB instance and if you would like to continue NCATS to host, you'll need to utilize the NCATS ITRB Pipeline. Is that okay for biothings?

If so, then biothings will take on the responsibility of moving the KGX files through the NCATS ITRB pipeline?

Are there other KPs that you can identify will also be part of this process? Thanks!

[kevinxin90]

@sstemann Hi Sarah, are there documentations which we can learn about NCATS ITRB Pipeline, so we can evaluate the feasibility?

Or maybe @newgene already have plans for that?

[newgene]

I also don't know about ITRB Pipeline. @sstemann we are happy to continue hosting BioThings-based KPs (for Service Provider, Multiomics Provider, Textmining Provider, and other teams) using NCATS cloud instances, so please advise what we need to work through the process. Thanks.

[sstemann]

Sure – we’re just starting the process (and I thought SmartAPI went through it with N3C. For now, we are targeting ITRB hosting dev by May 1 which supports continuous deployments, my understanding is that prod will not have CD but more of a staged/requested pipeline. https://docs.google.com/document/d/1DEHrRH-euvYCO8PrF4eyQjlOVp63mRFx99YvKYIjGR8/edit?usp=sharing The resources currently provided on this program have been NCATS but not part of ITRB, and may be sunsetted once everything is either ITRB or self-hosted with SLAs in place. https://docs.google.com/document/d/1DEHrRH-euvYCO8PrF4eyQjlOVp63mRFx99YvKYIjGR8/edit?usp=sharing From: Chunlei Wu <[email protected]> Sent: Friday, February 19, 2021 12:59 PM To: NCATSTranslator/TranslatorPM <[email protected]> Cc: Stemann, Sarah (NIH/NCATS) [C] <[email protected]>; Mention <[email protected]> Subject: Re: [NCATSTranslator/TranslatorPM] Multiomics - Server Question (#60) I also don't know about ITRB Pipeline. @sstemann<https://github.com/sstemann> we are happy to continue hosting BioThings-based KPs (for Service Provider, Multiomics Provider, Textmining Provider, and other teams) using NCATS cloud instances, so please advise what we need to work through the process. Thanks. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#60 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJEL5ITRWJV2D3KJTJEVGK3S72REXANCNFSM4XLXTQMQ>.

[newgene]

@sstemann awesome! Thanks. You are right, our team did have done this process for other projects relevant to N3C and CD2H. It just did not ring the bell when I heard the term "ITRB pipeline" :-)

We will plan it accordingly for our translator projects then. And since the BioThings stack from Service Provider provides the API hosting for other translator teams too. This effort should help reduce or even eliminate the overhead for other teams too.

[kevinxin90]

@sstemann Hi Sarah, @newgene and I would also like to explore the option of go with SLA. Could you share with us the agreement please? Thank you！