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10.1534/genetics.119.302777 #1283

Open bioentity-bot opened 5 years ago

bioentity-bot commented 5 years ago

https://bioentity.link//#/publication/10.1534/genetics.119.302777

bioentity-bot commented 5 years ago

https://bioentity.link//#/publication/10.1534/genetics.119.302777 @kyook New publication uploaded.

bioentity-bot commented 5 years ago

https://bioentity.link//#/publication/10.1534/genetics.119.302777 @kyook started curating

bioentity-bot commented 5 years ago

https://bioentity.link//#/publication/10.1534/genetics.119.302777 @kyook finished curating

suzialeksander commented 5 years ago

Having a lot of problems unlinking in this one. Particularly eL41 in the first paragraph- I want this linked later on in the paper, not most/all instances in this first paragraph. I used "Link all" in the first figure caption, it linked all previous occurrences, now I cannot unlink the first paragraph. Other entities (eL19) unlinked fine. Highlighting eL41 does not activate the link button, and clicking on the blue hyperlinked text does nothing. I have to highlight three characters of eL41 (no spaces), press the black link button, then escape the popup after doing nothing. Will create a bug report linking here.

suzialeksander commented 5 years ago

@kyook Now eL41 won't "Link all". Can someone maybe wipe this paper completely of all links and start again? I tried making sure I'm logged in, and I am.

To be honest, all the links are going to one of two possible proteins, as they're all paralogs so far, so in keeping with past practices nothing I've linked needs to have any links at all. I was linking to the more abundant of the two options, but in the past- say with histones- SGD did not mark up unless the authours defined which specific paralog was intended.

kyook commented 5 years ago

Hi Suzi,

I can take care of it, but it will take me a bit before I can get to a computer. In the meantime, if you want to, you can remove all linking by clicking “revert” in the right side panel then try linking the paper again. To link the paper choose sgd_gap from the keyword set drop down list and press link.

No worries if you can find the list, I’ll do it when I get a chance.

Kare

Sent from my iPhone

On Oct 31, 2019, at 15:32, suzialeksander notifications@github.com wrote:

 @kyook Now eL41 won't "Link all". Can someone maybe wipe this paper completely of all links and start again? I tried making sure I'm logged in, and I am.

To be honest, all the links are going to one of two possible proteins, as they're all paralogs so far, so in keeping with past practices nothing I've linked needs to have any links at all. I was linking to the more abundant of the two options, but in the past- say with histones- SGD did not mark up unless the authours defined which specific paralog was intended.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

bioentity-bot commented 5 years ago

https://bioentity.link//#/publication/10.1534/genetics.119.302777 @suzialeksander started curating

bioentity-bot commented 5 years ago

https://bioentity.link//#/publication/10.1534/genetics.119.302777 @kyook started curating

bioentity-bot commented 5 years ago

https://bioentity.link//#/publication/10.1534/genetics.119.302777 @kyook started curating

suzialeksander commented 5 years ago

@kyook I don't know if I marked up correctly, now the link is telling me

Pub locked by kyook

kyook commented 5 years ago

Hi @suzialeksander, are you able to access it now? I removed my name as an assignee, so it shouldn’t be locked by me now. Regardless, it looks like you do have access.

suzialeksander commented 5 years ago

Yes thanks!

From: Karen Yook notifications@github.com Sent: Friday, November 1, 2019 9:25 AM To: bioentity/papers papers@noreply.github.com Cc: Suzi Aleksander suzia@stanford.edu; Mention mention@noreply.github.com Subject: Re: [bioentity/papers] 10.1534/genetics.119.302777 (#1283)

Hi @suzialeksanderhttps://github.com/suzialeksander, are you able to access it now? I removed my name as an assignee, so it shouldn’t be locked by me now. Regardless, it looks like you do have access.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/bioentity/papers/issues/1283?email_source=notifications&email_token=ADIZNOEJS5TWQ3F3WIARZP3QRRJ7DA5CNFSM4JHKXA62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEC3NE5I#issuecomment-548852341, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADIZNOHBUVWYKYZQHKCY4J3QRRJ7DANCNFSM4JHKXA6Q.

suzialeksander commented 5 years ago

I can absolutely not get the entity eL41 to play nice. Link all doesn't link more than half, unlink doesn't change anything, now I can't unlink or link any instance of eL41. I'm left with stubs and delta symbols that are underlined & blue but the link icon is unresponsive. This is nonstandard nomenclature, is this why I'm still struggling with this paper? I tried to unlink every mention of the eL-named proteins in this paper (eL24, eL19) just to get it to the publisher. Not linking these entities is technically ok as they're paralogs and can't be tied to just one SGD ID, but it would be nice to link them to the more abundant of the identical paralogs.

kyook commented 5 years ago

Hi Suzie, can you skype right now?


Karen Yook

Curator / Editor
WormBase Caltech / microPublication
email: kyook@caltech.edu
email: karen@wormbase.org
email: karen.yook@micropublication.org
skype name: wbkaren
tel: +1(415)306-4150

On Fri, Nov 1, 2019 at 1:26 PM suzialeksander <notifications@github.com>
wrote:

> I can absolutely not get the entity eL41 to play nice. Link all doesn't
> link more than half, unlink doesn't change anything, now I can't unlink or
> link any instance of eL41. I'm left with stubs and delta symbols that are
> underlined & blue but the link icon is unresponsive. This is nonstandard
> nomenclature, is this why I'm still struggling with this paper? I tried to
> unlink every mention of the eL-named proteins in this paper (eL24, eL19)
> just to get it to the publisher. Not linking these entities is technically
> ok as they're paralogs and can't be tied to just one SGD ID, but it would
> be nice to link them to the more abundant of the identical paralogs.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <https://github.com/bioentity/papers/issues/1283?email_source=notifications&email_token=AAEVKGSO4ABFSI4DMQGLPLDQRSGGRA5CNFSM4JHKXA62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEC4CHCI#issuecomment-548938633>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AAEVKGSNR2MIGWS5J7G44MDQRSGGRANCNFSM4JHKXA6Q>
> .
>
kyook commented 5 years ago

Links to eL41 need to be removed and paper sent to publisher.

kyook commented 5 years ago

Hi Suzi,

it looks like there was a problem with the links being made and not stored in the db so they can't be removed, so a glitch that right now can't really be traced. The easiest thing to do right now is to send the paper to Sheridan and let them know during the proof stage (or you can write them now to warn them if you want) that all links to eL41 should be removed.

I will send it to the publisher.

Sorry for the trouble. Karen

nickstiffler commented 5 years ago

I updated the document with links to eL41 removed.

bioentity-bot commented 5 years ago

https://bioentity.link//#/publication/10.1534/genetics.119.302777

Link validation report

Validated Links

bioentity-bot commented 5 years ago

https://bioentity.link//#/publication/10.1534/genetics.119.302777 @kyook marked publication ready for publisher review. @Genetics-Database The article is now available on your server. @kyook

kyook commented 5 years ago

Hi @suzialeksander I downloaded the raw xml and deleted the links to eL41 then Nick uploaded the corrected file. I wasn't able to send the paper right away because there was a bad link to one of the rpl entities, there was no SGD ID attached, which caused a crash. It was not a problem, but in the future if you do notice that things aren't progressing when you hit send to publisher, it might be good to go through the links that are made - what I did was look through the list of objects linked in the sidebar and checked the ones with yellow warning symbols, I expanded each of the linked objects in the text and saw that one of them had an empty id. I deleted that link and relinked it with the id for the other similar objects.

suzialeksander commented 5 years ago

Thanks for the explanation @kyook . I saw the yellow symbol, clicked through probably a dozen or so individual links but I didn't know what I was looking for. I finally deduced the yellow warning was some of the links were to Protein lexicon, some were Gene, and the warning was because the actual text was identical. Next time I'll keep checking.