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AIRR Community Common Repository Working Group
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Pull request to merge changes approved at AIRR 2020 meeting #31

Closed bcorrie closed 2 years ago

bcorrie commented 3 years ago

@bussec @lgcowell (and others), for R13 and Epitopes, I know we want to encourage deposit in known DBs, but is IEDB the only one? Should this be a more general statement and use IEDB as an example? I am far from expert of course, but just wanted to confirm the wording, as it is very explicit where we are not so explicit any where else in this document...

lgcowell commented 3 years ago

Well, I think we are so explicit with ImmPort too.

My only thought about IEDB vs the others is I think IEDB has a careful curation process that is perhaps less rigorous with other resources, so I would personally hesitate to recommend the others. Christian correct me if I have the wrong impression.

bussec commented 3 years ago

I don't mind explicitly recommending IEDB in R13 as they are IMO providing excellent and systematically curated data and have put a lot of thought into their data models. However, I know that VDJdb also has TCR reactivity data, but I only had a look at it at superficial level. So we should probably flag this for review over the next year.

bussec commented 3 years ago

Regarding R14: Maybe there is something about ImmPort that I don't understand, but to me it is appears to be a just a repository in which your are obliged to publish your data if you receive funding from a certain funding body (in this case NIH). So R14 basically says that you should comply with your funding agreement. Therefore I was wondering whether we could use more generic language here...

bcorrie commented 3 years ago

I think more general language for R14 makes sense - I was always a bit confused about this... My understanding of ImmPort's "ImmPort"ance is that it provides a mechanism to store data that has sharing restrictions on the data. Should the focus of this recommendation be more around how to share data when such restrictions exist? Or is this more about advising researchers to link to AIRR-seq data in the ADC when it is relevant to their studies that are stored on ImmPort???

lgcowell commented 3 years ago

I think that makes sense. Recommend IEDB now and then review the others in the coming year to see if we want to recommend them as well.

Lindsay G. Cowell, PhD Division of Biomedical Informatics Department of Population and Data Sciences Department of Immunology University of Texas Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-9066

F4.218, MC9066 phone: 214-648-2289 fax: 214-648-2064 Lindsay.Cowell@utsouthwestern.edumailto:Lindsay.Cowell@utsouthwestern.edu

From: Christian Busse notifications@github.com Reply-To: airr-community/common-repo-wg reply@reply.github.com Date: Thursday, December 3, 2020 at 4:30 PM To: airr-community/common-repo-wg common-repo-wg@noreply.github.com Cc: Lindsay Cowell Lindsay.Cowell@UTSouthwestern.edu, Mention mention@noreply.github.com Subject: Re: [airr-community/common-repo-wg] Pull request to merge changes approved at AIRR 2020 meeting (#31)

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I don't mind explicitly recommending IEDB in R13 as they are IMO providing excellent and systematically curated data and have put a lot of thought into their data models. However, I know that VDJdbhttps://vdjdb.cdr3.net also has TCR reactivity data, but I only had a look at it at superficial level. So we should probably flag this for review over the next year.

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lgcowell commented 3 years ago

Yes, that’s true. We could potentially even drop this one. I think originally we were thinking about it in the following way. ImmPort doesn’t take sequencing data, so we were thinking if someone does repertoire sequencing as part of a study that otherwise has to be curated into ImmPort, then that person should put their AIRR-seq data in the AIRR DC and ensure that ImmPort links to that AIRR data. So it’s really not about encouraging people to curate their non-AIRR-seq into ImmPort so much as encouraging people to make sure that any ImmPort studies with an AIRR-seq component put that data in the AIRR DC (no different than our base recommendation) AND make sure that ImmPort links to the AIRR DC. So it is only the last bit that is different.

Lindsay G. Cowell, PhD Division of Biomedical Informatics Department of Population and Data Sciences Department of Immunology University of Texas Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-9066

F4.218, MC9066 phone: 214-648-2289 fax: 214-648-2064 Lindsay.Cowell@utsouthwestern.edumailto:Lindsay.Cowell@utsouthwestern.edu

From: Christian Busse notifications@github.com Reply-To: airr-community/common-repo-wg reply@reply.github.com Date: Thursday, December 3, 2020 at 4:38 PM To: airr-community/common-repo-wg common-repo-wg@noreply.github.com Cc: Lindsay Cowell Lindsay.Cowell@UTSouthwestern.edu, Mention mention@noreply.github.com Subject: Re: [airr-community/common-repo-wg] Pull request to merge changes approved at AIRR 2020 meeting (#31)

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Regarding R14: Maybe there is something about ImmPort that I don't understand, but to me it is appears to be a just a repository in which your are obliged to publish your data if you receive funding from a certain funding body (in this case NIH). So R14 basically says that you should comply with your funding agreement. Therefore I was wondering whether we could use more generic language here...

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/airr-community/common-repo-wg/pull/31#issuecomment-738390846, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABPC5BMEEW72LSIONNN3FVLSTAHNVANCNFSM4TL3ZCMA. CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.

UT Southwestern

Medical Center

The future of medicine, today.

lgcowell commented 3 years ago

The latter …

Lindsay G. Cowell, PhD Division of Biomedical Informatics Department of Population and Data Sciences Department of Immunology University of Texas Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-9066

F4.218, MC9066 phone: 214-648-2289 fax: 214-648-2064 Lindsay.Cowell@utsouthwestern.edumailto:Lindsay.Cowell@utsouthwestern.edu

From: Brian Corrie notifications@github.com Reply-To: airr-community/common-repo-wg reply@reply.github.com Date: Thursday, December 3, 2020 at 5:36 PM To: airr-community/common-repo-wg common-repo-wg@noreply.github.com Cc: Lindsay Cowell Lindsay.Cowell@UTSouthwestern.edu, Mention mention@noreply.github.com Subject: Re: [airr-community/common-repo-wg] Pull request to merge changes approved at AIRR 2020 meeting (#31)

EXTERNAL MAIL

I think more general language for R14 makes sense - I was always a bit confused about this... My understanding of ImmPort's "ImmPort"ance is that it provides a mechanism to store data that has sharing restrictions on the data. Should the focus of this recommendation be more around how to share data when such restrictions exist? Or is this more about advising researchers to link to AIRR-seq data in the ADC when it is relevant to their studies that are stored on ImmPort???

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/airr-community/common-repo-wg/pull/31#issuecomment-738452424, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABPC5BNHEBCJK4YLYFIFNSLSTAOHJANCNFSM4TL3ZCMA. CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.

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bcorrie commented 2 years ago

Hmmm @bussec it looks like this was never merged into master. We should merge this into master and then base our changes for 2022 off of that I believe... Would you agree?

bcorrie commented 2 years ago

Or I suppose we could branch 2022 off of 2020 and then merge them both into master after ratification at the AIRR meeting.