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10.1093/g3journal/jkad257 #1787

Open bioentity-bot opened 10 months ago

bioentity-bot commented 10 months ago

https://bioentity.link//#/publication/10.1093/g3journal/jkad257

bioentity-bot commented 10 months ago

https://bioentity.link//#/publication/10.1093/g3journal/jkad257 @kyook New publication uploaded.

suzialeksander commented 10 months ago

I can't get the https://bioentity.link... link to load, keeps timing out. Will try again tomorrow

kyook commented 10 months ago

Hi Suzie, It seems there is not a lot of memory for the server, or something like that. I suspect only one person can work on things at a time. On Nov 15, 2023, at 17:13, suzialeksander @.***> wrote: I can't get the https://bioentity.link... link to load, keeps timing out. Will try again tomorrow

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

kyook commented 10 months ago

Hi Suzie, please let us. know if you still have trouble today.

~~ 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, Nov 15, 2023 at 8:36 PM Karen Yook @.***> wrote:

Hi Suzie,

It seems there is not a lot of memory for the server, or something like that. I suspect only one person can work on things at a time.

On Nov 15, 2023, at 17:13, suzialeksander @.***> wrote:



I can't get the https://bioentity.link... link to load, keeps timing out. Will try again tomorrow

— Reply to this email directly, view it on GitHub https://github.com/bioentity/papers/issues/1787#issuecomment-1813499658, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEVKGQ7MLVHNWN5JBZ5XBDYEVLBNAVCNFSM6AAAAAA7GDTYDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJTGQ4TSNRVHA . You are receiving this because you were mentioned.Message ID: @.***>

nickstiffler commented 10 months ago

That was my fault. The server locked up when building a new keyword set, but it should be responding now.

kyook commented 10 months ago

Thanks Nick!

~~ 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 Thu, Nov 16, 2023 at 11:27 AM nickstiffler @.***> wrote:

That was my fault. The server locked up when building a new keyword set, but it should be responding now.

— Reply to this email directly, view it on GitHub https://github.com/bioentity/papers/issues/1787#issuecomment-1815007469, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEVKGWERLXWCUVWZOKYRKDYEZLKPAVCNFSM6AAAAAA7GDTYDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJVGAYDONBWHE . You are receiving this because you were mentioned.Message ID: @.***>

suzialeksander commented 10 months ago

I'm working on this, but it's very slow. I can now only add one link per time I open a tab at bioentity.link. If I try to add another, it lets me select text & drop the MOD ID but doesn't turn the text green. I have to reopen the https://bioentity.link//#/publication/10.1093/g3journal/jkad257 link between each entity. The alleles (variants) also aren't linking, I'm not sure if it's an incomplete list we provided (maybe lacking -Δ) or it's prioritizing the protein link before the variant? IE it's reading and linking ura3 before it sees the whole entity which is ura3-delta or ura3-Δ

suzialeksander commented 10 months ago

Screen Recording 2023-11-20 at 15.57.27.mov.zip

it's also just not letting me add links it should know

suzialeksander commented 10 months ago

I'm giving up again for the day. This has taken me hours and it's still not working. URA3, sgs1, others are not linking as in above video.

kyook commented 10 months ago

I'm so sorry @suzialeksander @nickstiffler is having a lot of trouble with the link editing. Would you take a look, she took a screen recording of her trials.

nickstiffler commented 10 months ago

It seems to work fine on my development machine, so I am guessing the problem is with the bioentity.link database. Would it be possible to try building a fresh keyword set to see if that resolves things?

kyook commented 10 months ago

I've reloaded the lexica (Gene, Variant, Protein, Strain). I remade the SGD_GeneOnly only Keyword set with just the Gene lexicon. @nickstiffler would you make the SGD_All Key Word Set with All the SGD lexica - SGD_Gene, SDG_Variant, SGD_Protein, SGD_Strain. Thank you!

nickstiffler commented 10 months ago

That keyword set is ready now.

suzialeksander commented 10 months ago

Just checking, I now get the error Unable to find publication '10.1093/g3journal/jkad257'! , was this paper moved to a new URL?

bioentity-bot commented 10 months ago

https://bioentity.link//#/publication/10.1093/g3journal/jkad257 @kyook New publication uploaded.

kyook commented 10 months ago

@suzialeksander The paper is here and linked now. When I updated all keyword sets, I deleted the old ones and that deleted the papers. I am having GSA resend the ones that got deleted, if you see the "Unable to find..." message, it means the paper isn't in the system and will have to be reloaded, just let me know.

bioentity-bot commented 9 months ago

https://bioentity.link//#/publication/10.1093/g3journal/jkad257

Link validation report

Validated Links

Invalidated Links

bioentity-bot commented 9 months ago

https://bioentity.link//#/publication/10.1093/g3journal/jkad257 @suzialeksander marked publication ready for publisher review. @Benet1983 The article is now available on your server. @kyook