Adding articles via DOI

[wrightmw]

This ticket will be specified to include supporting adding DOI (e.g preprints). We need to consider how preprints will be supported when added via DOIs.

[cgpreston]

SP ticket: https://broadinstitute.atlassian.net/browse/CSP-143

[wrightmw]

@courtneythaxton @ErinRiggs @marinadistefano We have a few questions for you about this project: 1) if someone added evidence via a preprint and then scored it, would you allow that classification to be published or would you expect the paper to be released first? i.e. would you allow preprints in published classification or should these be blocked from publication until the DOI has been replaced with its PMID 2) what types of DOI would you allow people to enter? e.g. restrict to preprint servers such as BioRXiv/MedRXiv and book articles 3) do you only want to add DOIs for adding new evidence to a GDM landing page, or do you want to use them throughout the GCI for adding other evidence too? e.g additional evidence about probands

[ErinRiggs]

Here are my thoughts:

1. I would allow preprints in a published classification - I would not want to delay the release of a curation until all pieces of evidence had been formally published. I would want a way to alert readers that a particular piece of evidence IS from a preprint, however.
2. I'm not familiar with other types of DOI, but definitely BioRXIV, MedRXiv, and book articles (though I suspect the latter would be exceedingly rare).
3. I'm not sure I understand this, but in general, I think anywhere that we allow PMIDs, we should also allow ClinVar IDs and DOIs. Of course the main place I am thinking of is the GDM landing page, but if there are other spots where PMIDs go, these other things should be able to go as well.

Erin Rooney Riggs, MS, CGC Assistant Professor Autism & Developmental Medicine Institute Geisinger @.***

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From: Matt W. Wright @.> Sent: Wednesday, May 25, 2022 12:28 PM To: ClinGen/gene-and-variant-curation-tools @.> Cc: Riggs, Erin @.>; Mention @.> Subject: [External] Re: [ClinGen/gene-and-variant-curation-tools] Adding articles via DOI (#1)

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@courtneythaxtonhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcourtneythaxton&data=05%7C01%7Ceriggs%40geisinger.edu%7Cf5ec6bdfec104d710dd008da3e73f990%7C37d46c567c664402a16055c2313b910d%7C0%7C0%7C637890965072681466%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=xpbQcNdwcNzLSZmwpq40Z39CGX0UvD5qLpLMNrxcDms%3D&reserved=0 @ErinRiggshttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FErinRiggs&data=05%7C01%7Ceriggs%40geisinger.edu%7Cf5ec6bdfec104d710dd008da3e73f990%7C37d46c567c664402a16055c2313b910d%7C0%7C0%7C637890965072681466%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wn3U0ONXdT0KvWwrIEXQTpdmVXBj9Xu1Onbdoqq%2FmTA%3D&reserved=0 @marinadistefanohttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmarinadistefano&data=05%7C01%7Ceriggs%40geisinger.edu%7Cf5ec6bdfec104d710dd008da3e73f990%7C37d46c567c664402a16055c2313b910d%7C0%7C0%7C637890965072681466%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=bqUp%2B41fbd7RWc9v%2BCV17XfpbBg%2BYXMP%2BhAGScWn4G8%3D&reserved=0 We have a few questions for you about this project:

1. if someone added evidence via a preprint and then scored it, would you allow that classification to be published or would you expect the paper to be released first? i.e. would you allow preprints in published classification or should these be blocked from publication until the DOI has been replaced with its PMID
2. what types of DOI would you allow people to enter? e.g. restrict to preprint servers such as BioRXiv/MedRXiv and book articles
3. do you only want to add DOIs for adding new evidence to a GDM landing page, or do you want to use them throughout the GCI for adding other evidence too? e.g additional evidence about probands

— Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FClinGen%2Fgene-and-variant-curation-tools%2Fissues%2F1%23issuecomment-1137600330&data=05%7C01%7Ceriggs%40geisinger.edu%7Cf5ec6bdfec104d710dd008da3e73f990%7C37d46c567c664402a16055c2313b910d%7C0%7C0%7C637890965072681466%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=BTuvZWnBLW954M%2BsIEKAs0kHfgbKjziYQTMzuDDAILY%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAHFJTFA5A4JSPIYGM7IX3JLVLZPLRANCNFSM5C367KHA&data=05%7C01%7Ceriggs%40geisinger.edu%7Cf5ec6bdfec104d710dd008da3e73f990%7C37d46c567c664402a16055c2313b910d%7C0%7C0%7C637890965072681466%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2B6yjkad1WPHSZ2AAO05xoa6LbfSmDj306f7AeKgWe6E%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

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[wrightmw]

Thanks @ErinRiggs ... can we add this as a discussion topic on an upcoming proxies call? Based on that discussion we can then do a mockup of the workflow and how this might look in the UI.

[ErinRiggs]

Of course! Copying in Taylor for agenda purposes.

Erin Rooney Riggs, MS, CGC Assistant Professor Autism & Developmental Medicine Institute Geisinger @.***

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From: Matt W. Wright @.> Sent: Wednesday, May 25, 2022 12:59 PM To: ClinGen/gene-and-variant-curation-tools @.> Cc: Riggs, Erin @.>; Mention @.> Subject: [External] Re: [ClinGen/gene-and-variant-curation-tools] Adding articles via DOI (#1)

External: Be careful with links and files. If suspicious, alert the Information Security Office. Questions? Call 570-271-8092

Thanks @ErinRiggshttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FErinRiggs&data=05%7C01%7Ceriggs%40geisinger.edu%7C58a3be5a34f14860b9e808da3e7845d7%7C37d46c567c664402a16055c2313b910d%7C0%7C0%7C637890983546032525%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=seIR%2BbX8SIeG5bbvTR4cVM5%2FOF%2FKyqUYJ2y0qjyDNnc%3D&reserved=0 ... can we add this as a discussion topic on an upcoming proxies call? Based on that discussion we can then do a mockup of the workflow and how this might look in the UI.

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[courtneythaxton]

I agree with Erin on her feedback. Definitely want to know a pre-print vs a book if possible, and if we can't get that detail, at least indicating the source (BioRXiv, GeneReviews, book etc.).

[tibingaman]

This has been added to our agenda. Thanks!