User talk:SCIdude

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Previous discussion was archived at User talk:SCIdude/Archive 1 on 2019-11-02.

Charles Matthews (talkcontribs)
SCIdude (talkcontribs)

Your decision to remove seems correct, why you would put it then on the human protein I don't understand, as MeSH treats it as family. I doubt that main subject statements are affected at all, as I did not use MeSH for them, do you have an example?

SCIdude (talkcontribs)
Charles Matthews (talkcontribs)

OK, thanks for the advice.

Reply to "Q29827740"
Daniel Mietchen (talkcontribs)

I'm glad to see that you are experimenting with bot work on citations and would be happy to help test these workflows and their output.

SCIdude (talkcontribs)

Yes, but I'm not planning large-scale operations at the moment. This is all in the context of SARS-Cov-2. One reason is that I'm scraping from PMC pages and I don't want to overdo that. However, that is probably also the most up-to-date source for this data, what do you think?

SCIdude (talkcontribs)
SCIdude (talkcontribs)

Oh I forgot. The output of it is to be fed to wikibase-cli like this: `wd ee --batch -s pmcart-cites --no-exit-on-error <output`.

SCIdude (talkcontribs)

Datapoint: of 25,668,149 items with DOI in a recent dump, 6,995,884 (27%) had at least one P2860 (cites work) statement.

Reply to "Bot for adding citations"
Reedy (talkcontribs)

Hello!

Your bot is logging into Wikimedia projects nearly 23K times in a 48H period, which is excessive, and shouldn't be necesssary.

See https://phabricator.wikimedia.org/T256533#6261565

Can you do anything about this?

https://www.mediawiki.org/wiki/API:Login#Additional_notes

>If you are sending a request that should be made by a logged-in user, add assert=user parameter to the request you are sending in order to check whether the user is logged in. If the user is not logged-in, an assertuserfailed error code will be returned.

SCIdude (talkcontribs)

Thanks, I'm investigating and reporting at phabricator.

Reply to "High Scidudebot login rate"

Invitation for the WikiProject COVID-19 call tomorrow (Monday, 15 of June)

1
TiagoLubiana (talkcontribs)

Hello SCIdude,

How are you? I hope things are all right.

I would like to invite you to the tomorrow (Monday, 15 of June) call of the Wikiproject COVID-19 at 15:00 UTC .

This is the link for the call: https://meet.google.com/vtp-ighz-npx

This is the link for the etherpad: https://etherpad.wikimedia.org/p/wikidata_covid_notes

The WikiProject seems to be losing momentum. Perception of the size of COVID-19 as an enormous problem is fading (at least in Brazil). That might be a sign of things getting better, but it is also very dangerous (as they might not be that better yet).

In tomorrow's call, I would like to discuss with you two important and related questions:

- How can this WikiProject best serve the anti-COVID-19 effort?

- What can this project offer for the post-COVID-19 Wikidata world?

As usual, if you have any topics to add, you can do so either before at the Project Meeting Page or at the meeting. or at the meeting.

I hope you can make it!

All the best,

Tiago


Reply to "Invitation for the WikiProject COVID-19 call tomorrow (Monday, 15 of June)"
Gobonobo (talkcontribs)

Hey SCIdude,


It looks like Scidudebot is erasing English aliases for items and replacing them with a single alias (the {{P|686}}). The changes I'm looking at occurred on 16 May (e.g. Q22282417, Q42982, Q30679). ~~~~

SCIdude (talkcontribs)
Gobonobo (talkcontribs)

I understand that you are erasing all aliases that aren't exact matches with the Gene Ontology database on thousands of items. So, aliases that originate from other databases and aliases that have been added by others are just being deleted. More importantly, article titles from the Wikipedias are also being deleted. On the item that links to the English Wikipedia article for "allergy", your bot erased the aliases "allergy" and "allergies". Those aliases still exist for all of the other languages, but now it is impossible to find the item for allergy through the dropdown menu.

SCIdude (talkcontribs)

Allergy is not type I hypersensitivity. In 2016 the item was wrongly merged with the allergy item. I'll move the type I hypersensitivity part to a separate item.

SCIdude (talkcontribs)
Reply to "Scidudebot aliases"
TiagoLubiana (talkcontribs)

Hello SCIdude,

How are you doing? Tomorrow (on Monday 20th ) we will have an open group in Google Meet to discuss the directions of the WikiProject COVID-19 and decide priorities to better organize the next steps.

You are more than invited to join us if you would like (and have the time) !

The call is scheduled for tomorrow 15 UTC, in this link: https://meet.google.com/tar-ufru-syb You can find more about it, and perhaps add your name to the list, here: Wikidata:WikiProject_COVID-19/Project_meeting

Thank you very much!

All the best,

Tiago

2A02:8109:9EC0:44B8:AD75:1F8B:A62E:837D (talkcontribs)

Hi Tiago, I'm immersed in biocuration for reactome.org and I won't hsve time at all for the meeting, sorry.

TiagoLubiana (talkcontribs)

I can imagine. Thanks for replying anyways!

Reply to "WikiProject COVID-19 meeting"
Bouzinac (talkcontribs)

Hello, I am afraid there are confusion possible between Q24774385, Q18258297 and Q15947987 , coud you please have a look?

SCIdude (talkcontribs)

First, the redirect does not need an item, so we can merge the item with the one where the redirect points to. Second, the link on the gene item is about the whole family (read first sentence) so we move the link to the family item. That's it, I guess. Thanks for the notice.

Reply to "Confusion possible"
TiagoLubiana (talkcontribs)

Just another public thanks for your contributions to the biology - related items on Wikidata:WikiProject_COVID-19/Items. Great work! If you have something specific you want some help with, please let me know :) ~~~~

Reply to "Thanks for your work on COVID19!"
Trade (talkcontribs)

I'm fairly certain you are not supposed to use archive URL like that.

This post was hidden by Trade (history)
Reply to "Re: InterPro release 77.0"

Q18031889 is missing a lot of data; not sure how to fix it

9
Seppi333 (talkcontribs)

I've been going through the gene article links in en:User:Certes/Gene_links#Other_links and came across the en:TRA (gene) article. The gene infobox looked pretty barren, so I figured it was connected to the wrong WD item, but the article is correctly linked to the entry for the gene in Homo sapiens: Q18031889. Based upon the UniProt entry for the gene at https://www.uniprot.org/uniprot/P0DSE1, it looks like PBB simply skipped a lot of stuff. I'm not that familiar with the bot on WD beyond what it imports; do you know if it can be manually activated to import the relevant data for this WD entry?

Seppi333 (talkcontribs)

Was going to say the same appears to be true for the TRB, TRD, and TRG entries on wikidata, but it occurred to me that they might simply be that way because those genes encode protein subunits.

2A02:8109:A140:E9A:299F:1124:2B54:850E (talkcontribs)

That is true. I haven't seen this before. You might want to post on the bot's talk page.

2A02:8109:A140:E9A:299F:1124:2B54:850E (talkcontribs)

I have an idea. You can try adding an encodes statement. Maybe the protein related info will appear. Sry I'm sick right now.

Seppi333 (talkcontribs)

Doesn't look like the protein entry exists on WD; this isn't really that big of an issue though since these genes just encode a group of T cell receptor subunits. I'll probably deal with it a little later if need be.

Anyway, I hope you feel better soon.

2A02:8109:A140:E9A:299F:1124:2B54:850E (talkcontribs)

But you said you looked at the UniProt entry so there must be a protein item. Thx.

SCIdude (talkcontribs)

Actually we should have it but we don't. Also the gene info is incomplete. This is a case for the bot.

Seppi333 (talkcontribs)
SCIdude (talkcontribs)
Reply to "Q18031889 is missing a lot of data; not sure how to fix it"