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10.1093/g3journal/jkae132 #1891

Open bioentity-bot opened 3 weeks ago

bioentity-bot commented 3 weeks ago

https://bioentity.link//#/publication/10.1093/g3journal/jkae132

bioentity-bot commented 3 weeks ago

https://bioentity.link//#/publication/10.1093/g3journal/jkae132 @kyook New publication uploaded.

kyook commented 2 weeks ago

HI @srengel I didn't have a chance to look carefully through this one. So you may have a lot of deletions to do. Apologies

kyook commented 2 weeks ago

apologies, it is this paper that isn't loading properly: https://bioentity.link/#/publication/10.1093/genetics/iyae093

~~ Karen Yook (she/her/hers) Executive Editor | Science Curator www.micropublication.org | www.wormbase.org California Institute of Technology cell: +1 (415) 306-4150

On Mon, Jun 17, 2024 at 9:00 AM Karen Yook @.***> wrote:

Hi Nick, This paper isn't loading in bioentity.link, Would you take a look? Thank you for your help. Karen

~~ Karen Yook (she/her/hers) Executive Editor | Science Curator www.micropublication.org | www.wormbase.org California Institute of Technology cell: +1 (415) 306-4150

On Sun, Jun 16, 2024 at 7:43 PM Link Bot @.***> wrote:

https://bioentity.link//#/publication/10.1093/g3journal/jkae132

— Reply to this email directly, view it on GitHub https://github.com/bioentity/papers/issues/1891, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEVKGRA5H4BEUN4RCS4ZHTZHY5LZAVCNFSM6AAAAABJNC5HXCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM2TMMJVG44DCMQ . You are receiving this because you were mentioned.Message ID: @.***>

kyook commented 2 weeks ago

The problem is this ext-link that has no text: <ext-link ext-link- type="uri" xlink:href="http://academic.oup.com/genetics/article-lookup/doi/10.1093/genetics/iyae093#supplementary-data"/

I can update the code to handle this, but it seems like it might be an error in their xml.

Nick

On Mon, 2024-06-17 at 09:06 -0600, Karen Yook wrote:

apologies, it is this paper that isn't loading properly: https://bioentity.link/#/publication/10.1093/genetics/iyae093

~~ Karen Yook (she/her/hers) Executive Editor | Science Curator  www.micropublication.org | www.wormbase.org California Institute of Technology cell: +1 (415) 306-4150

On Mon, Jun 17, 2024 at 9:00 AM Karen Yook @.***> wrote:

Hi Nick,  This paper isn't loading in bioentity.link, Would you take a look?  Thank you for your help. Karen

~~ Karen Yook (she/her/hers) Executive Editor | Science Curator  www.micropublication.org | www.wormbase.org California Institute of Technology cell: +1 (415) 306-4150

On Sun, Jun 16, 2024 at 7:43 PM Link Bot @.***> wrote:

https://bioentity.link//#/publication/10.1093/g3journal/jkae132 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

kyook commented 2 weeks ago

Ok, I will ask them to reupload it. Thank you for looking!

~~ Karen Yook (she/her/hers) Executive Editor | Science Curator www.micropublication.org | www.wormbase.org California Institute of Technology cell: +1 (415) 306-4150

On Mon, Jun 17, 2024 at 3:18 PM Nicholas Stiffler < @.***> wrote:

The problem is this ext-link that has no text: <ext-link ext-link- type="uri" xlink:href=" http://academic.oup.com/genetics/article-lookup/doi/10.1093/genetics/iyae093#supplementary-data "/

I can update the code to handle this, but it seems like it might be an error in their xml.

Nick

On Mon, 2024-06-17 at 09:06 -0600, Karen Yook wrote:

apologies, it is this paper that isn't loading properly: https://bioentity.link/#/publication/10.1093/genetics/iyae093

~~ Karen Yook (she/her/hers) Executive Editor | Science Curator www.micropublication.org | www.wormbase.org California Institute of Technology cell: +1 (415) 306-4150

On Mon, Jun 17, 2024 at 9:00 AM Karen Yook @.***> wrote:

Hi Nick, This paper isn't loading in bioentity.link, Would you take a look? Thank you for your help. Karen

~~ Karen Yook (she/her/hers) Executive Editor | Science Curator www.micropublication.org | www.wormbase.org California Institute of Technology cell: +1 (415) 306-4150

On Sun, Jun 16, 2024 at 7:43 PM Link Bot @.***> wrote:

https://bioentity.link//#/publication/10.1093/g3journal/jkae132 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

bioentity-bot commented 2 weeks ago

https://bioentity.link//#/publication/10.1093/g3journal/jkae132 @srengel started curating

bioentity-bot commented 2 weeks ago

https://bioentity.link//#/publication/10.1093/g3journal/jkae132 @srengel finished curating

srengel commented 2 weeks ago

Hi @kyook there is no big yellow button to 'send to publisher' on this one. ??

kyook commented 2 weeks ago

Thank you @srengel, I will deal with it.

kyook commented 2 weeks ago

We have an issue with sending this paper to your server, so I am attaching the linked file here.

~~ Karen Yook (she/her/hers) Executive Editor | Science Curator www.micropublication.org | www.wormbase.org California Institute of Technology cell: +1 (415) 306-4150

On Wed, Jun 19, 2024 at 10:26 AM Stacia Engel @.***> wrote:

Hi @kyook https://github.com/kyook there is no big yellow button to 'send to publisher' on this one. ??

— Reply to this email directly, view it on GitHub https://github.com/bioentity/papers/issues/1891#issuecomment-2179086411, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEVKGRIV6FVIBRMWYY4IPTZIGWMNAVCNFSM6AAAAABJNC5HXCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZZGA4DMNBRGE . You are receiving this because you were mentioned.Message ID: @.***>

bioentity-bot commented 2 weeks ago

https://bioentity.link//#/publication/10.1093/g3journal/jkae132

Link validation report

Validated Links

Invalidated Links

bioentity-bot commented 2 weeks ago

https://bioentity.link//#/publication/10.1093/g3journal/jkae132 @kyook marked publication ready for publisher review. @Benet1983 The article is now available on your server. @kyook

kyook commented 2 weeks ago

Apologies, I found a workaround, it should be on your server now.

~~ Karen Yook (she/her/hers) Executive Editor | Science Curator www.micropublication.org | www.wormbase.org California Institute of Technology cell: +1 (415) 306-4150

On Wed, Jun 19, 2024 at 10:33 AM Karen Yook @.***> wrote:

We have an issue with sending this paper to your server, so I am attaching the linked file here.

~~ Karen Yook (she/her/hers) Executive Editor | Science Curator www.micropublication.org | www.wormbase.org California Institute of Technology cell: +1 (415) 306-4150

On Wed, Jun 19, 2024 at 10:26 AM Stacia Engel @.***> wrote:

Hi @kyook https://github.com/kyook there is no big yellow button to 'send to publisher' on this one. ??

— Reply to this email directly, view it on GitHub https://github.com/bioentity/papers/issues/1891#issuecomment-2179086411, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEVKGRIV6FVIBRMWYY4IPTZIGWMNAVCNFSM6AAAAABJNC5HXCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZZGA4DMNBRGE . You are receiving this because you were mentioned.Message ID: @.***>

kyook commented 2 weeks ago

This paper is primarily a non-S. cerevisiae paper. most links were removed. When opening the paper in the linker, there was no link table visible, also there was no indication that a keyword set was run, and there was no Send to Publisher button visible. I don't know if this is related, but I ran the linker using an innocuous keyword set (Editorial Check). Upon refresh, the link table showed up with an indication that the SGD gene keyword and Editorial Check sets had been run. The only entities showed were the remaining few SGD links, which weren't there before. The Send to Publisher button showed up again. I saw this with other articles where no keyword set had been 'run' or the paper reverted after running a keyword set.