User talk:Egon Willighagen

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User talk Archives[edit]

Re: Plz check for duplicates[edit]

Thank you Egon for the information. While revewing my last entries, I'm trying to merge two items (8-Chloro-1-octene and 8-Chlorooct-1-ene) but when attempting it I receive the following message: Currently only Qid/Lid is a valid input and I can't continue. Do you know how to solve it?--Fran Ara (talk) 09:25, 30 January 2020 (UTC)

Just solved it, using the Q-number instead of the item name. Thank you anyway.--Fran Ara (talk) 09:34, 30 January 2020 (UTC)

DSSTOX compound identifier[edit]

I found that we do not have a property for this.--GZWDer (talk) 15:27, 30 January 2020 (UTC)

WikiCite Satellite Cologne 2020[edit]

Hi Egon - you have added yourself to the list of people who are interested in the WikiCite Satellite Cologne 2020 meeting. The call for submissions is still open and we would love to see your contribution! Let me know if you have any questions. Best wishes!

Konrad Foerstner (talk) 18:18, 12 February 2020 (UTC)

WikiProject COVID-19 meeting[edit]

Hello Egon,

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, decide priorities better to organize the next steps.

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

The talk 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,

TiagoLubiana (talk) 23:50, 19 April 2020 (UTC)

Call Wikiproject COVID-19 tomorrow (Monday, May 4th)[edit]

Hello Egon,

How are you doing?

I am here to invite you for the Wikiproject COVID-19 call tomorrow (Monday, May 4th). If you are able to meet, the call (in this link: https://meet.google.com/vtp-ighz-npx) will happen tomorrow at 15:00 UT.

As a note, 15:00 UTC is:

  • 11:00 AM in New York, USA
  • 12:00 AM in São Paulo, Brazil
  • 4:00 PM in Tunisia
  • 6:00 PM Eastern European Summer Time (EEST)

If you want, also feel free to add topics at the meeting page!

Cheers, TiagoLubiana (talk) 22:29, 3 May 2020 (UTC)

Call Wikiproject COVID-19 tomorrow (Monday, May 18th)[edit]

Hello Egon,

How are you doing?

I am here (once again)to invite you for the Wikiproject COVID-19 call tomorrow (Monday, May 18th).

Have you been working on COVID-19 related things in the past few weeks?

If you are able to meet, the call (in this link: https://meet.google.com/vtp-ighz-npx) will happen tomorrow at 15:00 UT.

As a note, 15:00 UTC is:

  • 11:00 AM in New York, USA
  • 12:00 AM in São Paulo, Brazil
  • 4:00 PM in Tunisia
  • 6:00 PM Eastern European Summer Time (EEST)

If you want, also feel free to add topics at the meeting page!

Cheers, TiagoLubiana (talk) 23:50, 17 May 2020 (UTC)

Wikiproject COVID-19 call tomorrow (1st of June)[edit]

Hello, Egon,

How are you doing?

This is a friendly reminder of (and an invitation for) tomorrow's (Monday, 01 of June) Wikiproject meeting, at 15:00 UTC as usual, and at the usual link: https://meet.google.com/vtp-ighz-npx .


I was wondering from the biological perspective, which are the gaps that you see on Wikidata (related to COVID-19, more specifically). I am thinking of ways how the project can be of greater help to the bio community.

If you want to add something to the agenda in advance, feel free to just edit Wikidata:WikiProject_COVID-19/Project_meeting.

I hope you can make it! :)

Best,

TiagoLubiana (talk) 20:39, 31 May 2020 (UTC)


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

Hello Egon,

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

TiagoLubiana (talk) 00:38, 15 June 2020 (UTC)

Interview Invitation[edit]

Greetings,

I noticed your editing stats in Wikidata, which led me to look up your profile. Thank you for all the great work!

I’m reaching out to you because I’m working on a research project about understanding what motivates editors like you to contribute to Wikidata. We’re also interested in learning about how you feel your contributions are being used outside of Wikidata. Since you are such an active community member, I thought you might also be interested in helping to build the broader community’s knowledge about Wikidata, and why it matters.

If you’re interested, let’s schedule a time to talk over Zoom, or whichever platform you prefer. If you are interested, please fill in a questionnaire. The conversation should take about 30 min.

Hope you have a great day,

Chuankaz (talk) 14:49, 14 July 2020 (UTC)

protein family membership[edit]

Hi Egon, about the SARS-Cov-2 proteins, Pfam ID is for protein family items, not their members. For the members, if you look at how the bot does it for all other proteins, we say protein-->part of-->family item. --SCIdude (talk) 15:39, 22 July 2020 (UTC)

Hi @SCIdude: sorry for the late reply. I will look into it. --Egon Willighagen (talk) 06:38, 25 July 2020 (UTC)
So far, I: 1. created a EntitySchema for protein family: https://www.wikidata.org/wiki/EntitySchema:E233 2. updated spike glycoprotein [SARS-CoV-2] (Q87917585), but for this I had to create two missing Pfam entries. This is a problem. How complete is Pfam in Wikidata? --09:07, 25 July 2020 (UTC)
Not very. The canonical database in WD is InterPro. Also, Pfam is a subset of InterPro, as far as I am aware. The InterPro import is also quite recent. As to Cov-2 there is a list of family items at the Cov-2 project to chose from. Moreover, in principle it's already automated: the bot should create these statements from the resp. UniProt data, no idea why it does not do it here. --SCIdude (talk) 13:49, 25 July 2020 (UTC)
Okay, then I'll check InterPro ID (P2926) too next time. I know created Coronavirus S2 glycoprotein family (Q97662399) which has the InterPro ID (P2926) already used on another item too. But when doing this, I noticed a third item for the InterPro ID (P2926) of that one and I wonder if they should be unique. Should they? Because you created Spike receptor binding domain, protein family (Q83136543) which has the same InterPro ID (P2926) as Spike receptor binding domain (Q24738749). Can you first let me know the same InterPro ID (P2926) value should only be on one Wikidata item? If so, is there a reason why that is not a constraint? Should it not? Let's keep talking and get this right. --15:00, 25 July 2020 (UTC)
You have seen the P31 statements on each of the two? One is a domain, one the associated family. InterPro has this ambiguity that its domain entries actually represent families. So there are two items that link to "InterPro domains". If a constraint is needed a complex constraint could take this ambiguity into account. --SCIdude (talk) 04:24, 26 July 2020 (UTC)
So, how is that modeled right now? From what you say, I'd expect items of InterPro ID (P2926) to have two different types (instance of (P31)). That may not be easy to express as constraint, but should not be hard to do that as ShEx. How about creating two ShEx then, one for InterPro Domain and the other for InterPro Family (or something like that)? --Egon Willighagen (talk) 06:27, 26 July 2020 (UTC)
I have no idea about ShEX but the design sounds good. --SCIdude (talk) 07:32, 26 July 2020 (UTC)
Okay, all four incorrect uses have now been fixed, see https://w.wiki/XsY --Egon Willighagen (talk) 11:29, 26 July 2020 (UTC)
Thanks! --SCIdude (talk) 14:15, 26 July 2020 (UTC)

Hi Egon, I finally updated your EntitySchema:E233 to what is the common case in WD. I'll continue with shapes as I want to have a basic set of shapes that define a molbio slice of WD. --SCIdude (talk) 15:52, 12 December 2020 (UTC)

@SCIdude: great! There is a growing overview here: https://www.wikidata.org/wiki/Wikidata:Database_reports/EntitySchema_directory#chemistry --Egon Willighagen (talk) 16:15, 13 December 2020 (UTC)

P31/P279 cycle in on fatty acyl-CoA (Q33616143)[edit]

It looks like fatty acyl-CoA (Q33616143) is a subclass of acyl-CoA (Q2699537) which is an instance of fatty acyl-CoA (Q33616143). Should these two items be merged? --Cdo256 (talk) 17:01, 9 September 2020 (UTC)

No, this needs a fix. Acyl is the residue of any carbonic acid, of which fatty acids are a subset. You can also see this expressed in ChEBI as "fatty acyl-CoA is a Acyl-CoA". It is true that most acyl-CoAs in biological systems are fatty, and so these are often used as synonyms, but it is wrong usage. --SCIdude (talk) 04:39, 10 September 2020 (UTC)
Done. Thanks for noticing! --SCIdude (talk) 04:55, 10 September 2020 (UTC)
Yes, that circular subclassing sounds like a bug to me too. I agree with the explanation of SCIdude. And thanks for reporting indeed. --Egon Willighagen (talk) 05:31, 10 September 2020 (UTC)

Compounds without defined stereochemistry[edit]

Hi, in December 2019 you wrote a script to find all compounds with missing stereochemistry. What is the current status of this? Is it possible to use this script to change instance of (P31) chemical compound (Q11173) to instance of (P31) group of stereoisomers (Q59199015) + subclass of (P279) chemical compound (Q11173) (bot/QS), at least for more than a few hundred, maybe a few thousand items? Wostr (talk) 18:41, 25 September 2020 (UTC)

@Wostr:, thanks for asking. I had the code running on our groups Jenkins server, but the 2019 cyber attack at Maastricht University took it out. While our work was not directly involved, we were affected by the new regulations and are still recovering from that. The scripts are online here: https://github.com/egonw/ons-wikidata/tree/master/Wikidata The output of the scripts so far has always been new statements; I do not currently know how to use QuickStatements to remove statements (only theoretically). It's been a bit busy here, and not sure when I get to it again, but will try to run the script later this weekend and put the output somewhere (and link here). --Egon Willighagen (talk) 08:38, 26 September 2020 (UTC)

We sent you an e-mail[edit]

Hello Egon Willighagen,

Really sorry for the inconvenience. This is a gentle note to request that you check your email. We sent you a message titled "The Community Insights survey is coming!". If you have questions, email surveys@wikimedia.org.

You can see my explanation here.

MediaWiki message delivery (talk) 18:45, 25 September 2020 (UTC)

Items for PubMed articles[edit]

Items for PMID < 32240000 is 100% complete and < 33260000 is 99% complete. Please do not create any more items. Search the PMID in search box (like this) will find the item.--GZWDer (talk) 17:01, 3 December 2020 (UTC)

  • Hi, al always do check if there already is an item. I'll try to figure out what went wrong and why I did not find it (with the tools I use). Sorry for the inconvenience. --Egon Willighagen (talk) 17:11, 3 December 2020 (UTC)

Entries with multiple canonical SMILES[edit]

Egon,

I found a few entries with duplicate canonical SMILES that were edited with quickstatements on your account: http://www.wikidata.org/entity/Q77625089 http://www.wikidata.org/entity/Q77508693 … I have ~ 20 or 30 of them. I can give you the full list if you need. Bjonnh (talk) 04:03, 2 January 2021 (UTC)

Yes, please send them. It seems in these cases my script did not detect that there already was a SMILES. It is not wrong: SMILES are not unique and Wikidata does not specific how to canonicalize SMILES. Thanks for the heads-up. --Egon Willighagen (talk) 07:26, 2 January 2021 (UTC)

http://www.wikidata.org/entity/Q75064493 http://www.wikidata.org/entity/Q75053148 http://www.wikidata.org/entity/Q75063027 http://www.wikidata.org/entity/Q75057975 http://www.wikidata.org/entity/Q77309963 http://www.wikidata.org/entity/Q77280667 http://www.wikidata.org/entity/Q77372598 http://www.wikidata.org/entity/Q77375049 http://www.wikidata.org/entity/Q77280985 http://www.wikidata.org/entity/Q77310912 http://www.wikidata.org/entity/Q77373816 http://www.wikidata.org/entity/Q77378734 http://www.wikidata.org/entity/Q77381090 http://www.wikidata.org/entity/Q77382605 http://www.wikidata.org/entity/Q77520115 http://www.wikidata.org/entity/Q77518548 http://www.wikidata.org/entity/Q77567693 http://www.wikidata.org/entity/Q77566384 http://www.wikidata.org/entity/Q77520662 http://www.wikidata.org/entity/Q77625089 http://www.wikidata.org/entity/Q77508693 http://www.wikidata.org/entity/Q77490238 http://www.wikidata.org/entity/Q77509037 http://www.wikidata.org/entity/Q77513680

Also I'm wondering why I didn't get an alert that you replied to that comment. any idea?

Bjonnh (talk) 18:23, 2 January 2021 (UTC)

@Bjonnh: I think you only get an alert of you either watch this page or if I ping you with {{Ping}}. Thanks for the list! Now that the Bacting paper rebuttal is almost done, I will work on Bacting (Bioclipse) scripts for curation lists of chemistry in Wikidata again, and will make this one too. --Egon Willighagen (talk) 08:06, 3 January 2021 (UTC)
Okay, they should all be fixed now. Good news: it does not seem a problem of my code and well contained. Instead, it looks like a timing issues. The NPImporterBot added SMILES in between my code detecting a missing SMILES and adding it. --Egon Willighagen (talk) 08:56, 3 January 2021 (UTC) Weirdly, I'm watching the page and didn't got your ping nor anything… This is weird, I'll check if there are some notification settings I may have changed. Congrats on that Bacting paper, I just had a look at your code a bit, I'll have to look at bioclipse a bit more. Bjonnh (talk) 16:29, 4 January 2021 (UTC)