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10.1093/genetics/iyad199 #1793

Open bioentity-bot opened 8 months ago

bioentity-bot commented 8 months ago

https://bioentity.link//#/publication/10.1093/genetics/iyad199

bioentity-bot commented 8 months ago

https://bioentity.link//#/publication/10.1093/genetics/iyad199 @kyook New publication uploaded.

kyook commented 7 months ago

@suzialeksander this paper needs to be reloaded before you can look at it. i will let you know when it is uploaded again.

bioentity-bot commented 7 months ago

https://bioentity.link//#/publication/10.1093/genetics/iyad199 @kyook New publication uploaded.

kyook commented 7 months ago

Hi @suzialeksander, the paper should be ready for you now. I reloaded all the lexica and Nick rebuilt the SGD_ALL keywordset, which is the one I used to link this paper, so other entities will be linked as well. I hope this is seamless for you. I really am sorry about all of the trouble.

suzialeksander commented 7 months ago

OK, this paper sort of has all the links. The SGD IDs are attached, but the linking isn't working- for example, pcf11-13 is recognised as being linked in the Fig. 1 caption box, and I did "link all occurrences". But a later link turns green with no entity found. Also, these allele links aren't working as they should, the link is https://www.yeastgenome.org/allele/S000305897 not https://www.yeastgenome.org/locus/S000305897

I'm preparing new files to be linked and will email them to @kyook, not sure if this will fix the above issue but it will provide an updated list of SGDIDs

Screenshot 2023-12-05 at 17 43 28
nickstiffler commented 7 months ago

I updated the lexicon source url so the allele links should be working now, but I will need to investigate why the other links aren't being saved to the server.

suzialeksander commented 7 months ago

I'm still getting the green linked pcf11-13/S000305897 not linked error as in the screenshot above.

suzialeksander commented 7 months ago

Note for publisher: the paper uses the reserved name RFQ1 but that name has not yet been standardized and could end up not being used if it's not published as officially the name for YDR124W. Unless there's reason to believe such a publication is already being processed, the YDR124W name should be used (and linked to SGD GENE S000002531)

There is also an occurrence of pcf1-DNL that should probably be pcf11-DNL and linked as the other occurrences are

nickstiffler commented 7 months ago

That error just means the link isn't being saved to the server for some unknown reason. The link does exist in the XML so it should be still be valid for the publisher.

kyook commented 7 months ago

OK, this paper sort of has all the links. The SGD IDs are attached, but the linking isn't working- for example, pcf11-13 is recognised as being linked in the Fig. 1 caption box, and I did "link all occurrences". But a later link turns green with no entity found. Also, these allele links aren't working as they should, the link is https://www.yeastgenome.org/allele/S000305897 not https://www.yeastgenome.org/locus/S000305897

hi @suzialeksander was there a lot of editing for this paper? If not, then I can will go ahead and relink it, which should contain the updated link path (allele vs locus) URL. If there was a lot of editing, then it would have to be edited again, however I can try to do it as I have your link list.

For future reference for both of us, if there is a linked entity in the paper and that message of the entity not being found comes up, it is still ok to send the paper back to GSA. That linking instance will just not be stored in BioEntity.link.

nickstiffler commented 7 months ago

There shouldn't be a need to re-link as the redirect happens at bioentity.link.

kyook commented 7 months ago

But you updated the Lexica info, Does that not need the article to be relinked?

kyook commented 7 months ago

I'm still seeing the links open on the website with the locus URL construction form https://yeastgenome.org/locus/S000002636 it should be https://yeastgenome.org/allele/ ID

bioentity-bot commented 7 months ago

https://bioentity.link//#/publication/10.1093/genetics/iyad199

Link validation report

Validated Links

Invalidated Links

bioentity-bot commented 7 months ago

https://bioentity.link//#/publication/10.1093/genetics/iyad199 @suzialeksander marked publication ready for publisher review. @Benet1983 The article is now available on your server. @kyook

suzialeksander commented 7 months ago

@kyook I think, the only issue is these funny pcf11-13 links. The rest are all linked and present and so I've submitted the paper, was that correct?

kyook commented 7 months ago

@suzialeksander yes, perfect. Thank you!!!!

nickstiffler commented 7 months ago

But you updated the Lexica info, Does that not need the article to be relinked?

In most cases the link is set to identifiers.org, so bioentity.link will handle the redirect. The exceptions are pombe and some of the wormbase lexica.

nickstiffler commented 7 months ago

I'm still seeing the links open on the website with the locus URL construction form https://yeastgenome.org/locus/S000002636 it should be https://yeastgenome.org/allele/ ID

I think that is a gene, so the old link is still correct.