User talk:Egon Willighagen/Archive 2019

sn-glycero-3-phosphocholine (Q28529699)

Hi Egon. Could you please check whether or not sn-glycero-3-phosphocholine (Q28529699) (created by you) is a duplicate of glycerylphosphorylcholine (Q2706622)? --Leyo 01:05, 2 January 2019 (UTC)

@Leyo: OK, it's on my radar. The have different InChIKey's and it's the stereochemistry in which they differ. I'll try to clean it up later (checking all linked identifiers. --Egon Willighagen (talk) 08:04, 2 January 2019 (UTC)

Thank you. I am trying to resolve the issues listed there. --Leyo 12:59, 3 January 2019 (UTC)

@Leyo:, solved. See also https://tools.wmflabs.org/scholia/chemical-class/Q2706622 --Egon Willighagen (talk) 11:32, 7 January 2019 (UTC)

Thank you. --Leyo 13:39, 7 January 2019 (UTC)

Please support the Sustainability Initiative!

Please support the Sustainability Initiative!

Hello Egon Willighagen, I saw that you are one of the authors of the Greta Thunberg (Q56434717) item. Because I am looking for ways to reduce the environmental impact of Wikipedia itself, I wanted to ask you to check out the Sustainability Initiative and to add your name to the list of supporters so that I can show that many community members are behind this effort. Thanks! --Gnom (talk)

@Gnom:, thanks, done! I didn't know about this. Umm, can I also point you in return to https://docs.google.com/document/d/14GycQnHwjIQBQrtt6pyN-ZnRlX1n8chAtV72f0dLauU/edit# then? This Feedback to Plan S is about to future of scholarly communication. Please have a look. It is my strong belief that we can do a lot by making our scholarly journals better, to better support open science, which at least would reduce the amount of (energy consuming) redundant research. We have two days left to get this Feedback co-signed by as many people as possible, before I need to submit it to cOAlition S. --Egon Willighagen (talk) 11:42, 4 February 2019 (UTC)

‎Your modification:

Hello Egon Willighagen,

Why did you delete single-value constraint (Q19474404) from MassBank accession ID (P6689) ? --Eihel (talk) 15:08, 24 April 2019 (UTC)

@Eihel:Because each compound can have one or more Massbank entries. Did I remove the wrong one?? --Egon Willighagen (talk) 15:23, 24 April 2019 (UTC)

Do you have an example? A component has a spectrometry with a single graph. In the caffeine example, it is only caffeine (no milk has been added ). If you think of ions, another Item must be in WD (or create one). If you think of different acetate, you can only add the strict compound with a single WD Item. etc. Attention, it is only the entries Massbank, not entries MONA or other: access from the URL and the RegEx given in the Property. Do not confuse with distinct-values constraint (Q21502410)? Has anyone in Norman made several specetrometrics on a single substance? Several labs, yes, but only one Massbank ID must be available having the form of the RegEx given in MassBank accession ID (P6689). If multiple MassBank IDs exist for a single substance, one of the two must be out of date. --Eihel (talk) 16:04, 24 April 2019 (UTC)

The Massbank Access ID is not an identifier for the chemical, but for the record in the database. There can be multiple spectra in Massbank for caffeine, and there are. See for example https://massbank.eu/MassBank/Result.jsp?compound=caffeine&op1=and&mz=&tol=0.3&op2=and&formula=&type=quick&searchType=keyword&sortKey=not&sortAction=1&pageNo=1&exec=&inst_grp=ESI&inst=CE-ESI-TOF&inst=ESI-ITFT&inst=ESI-ITTOF&inst=ESI-QTOF&inst=ESI-TOF&inst=LC-ESI-IT&inst=LC-ESI-ITFT&inst=LC-ESI-ITTOF&inst=LC-ESI-Q&inst=LC-ESI-QFT&inst=LC-ESI-QIT&inst=LC-ESI-QQ&inst=LC-ESI-QTOF&inst=LC-ESI-TOF&ms=all&ms=MS&ms=MS2&ms=MS3&ms=MS4&ion=0 I read the definitions of the two contraints again, and I think I got them right. So, each Massbank Accession ID can have only one compound, but each compound can have more than one accession ID. --Egon Willighagen (talk) 16:10, 24 April 2019 (UTC)

You are right, sorry for the inconvenience --Eihel (talk) 16:16, 24 April 2019 (UTC)

No problem at all! Peer review in action :) --Egon Willighagen (talk) 16:21, 24 April 2019 (UTC)

Community Insights Survey

Share your experience in this survey

Hi Egon Willighagen/Archive 2019,

The Wikimedia Foundation is asking for your feedback in a survey about your experience with Wikidata and Wikimedia. The purpose of this survey is to learn how well the Foundation is supporting your work on wiki and how we can change or improve things in the future. The opinions you share will directly affect the current and future work of the Wikimedia Foundation.

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Sincerely,

RMaung (WMF) 17:38, 10 September 2019 (UTC)

Reminder: Community Insights Survey

Share your experience in this survey

Hi Egon Willighagen/Archive 2019,

A couple of weeks ago, we invited you to take the Community Insights Survey. It is the Wikimedia Foundation’s annual survey of our global communities. We want to learn how well we support your work on wiki. We are 10% towards our goal for participation. If you have not already taken the survey, you can help us reach our goal! Your voice matters to us.

Please take 15 to 25 minutes to give your feedback through this survey. It is available in various languages.

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Sincerely,

RMaung (WMF) 19:54, 20 September 2019 (UTC)

Duplicate PubChem IDs

I noticed that you created many chemical compound items on Sept 18 that have the PubChem ID listed twice (https://www.wikidata.org/w/index.php?title=Wikidata:Database_reports/Constraint_violations/P662&diff=1020077575&oldid=1009421759). Is there an easy way of removing the duplicates in an automated way, or do they need to be fixed manually? Regards, Edgar181 (talk) 15:35, 3 October 2019 (UTC)

Oh, carp. Sorry! I am not aware of an easy way. But I'll fix it. Thanks for the notice! --Egon Willighagen (talk) 15:46, 3 October 2019 (UTC)

@Edgar181: okay I think I got them all fixed now. Thanks again for point out the issue. --Egon Willighagen (talk) 09:46, 4 October 2019 (UTC)

That was quick. Thanks. Edgar181 (talk) 11:20, 4 October 2019 (UTC)

Q70000000

Item 70 million is yours! Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 12:00, 8 October 2019 (UTC)

Yeah, I know ;) --Egon Willighagen (talk) 12:02, 8 October 2019 (UTC)

your found in taxon statements from Recon

Hi Egon, Found in taxon should have as value the set of all taxa where this is true, not one unimportant example. Otherwise I go through all substances in Mycobacterium tuberculosis and create statements too, see? I think the stmts are really bad, and you should remove them. --SCIdude (talk) 06:55, 20 October 2019 (UTC)

Hi @SCIdude:, I understand your point very well, and generally don't disagree, but I tend to disagree on the specific example: We want statements backed by literature and/or databases. It is not the task of Wikidata to infer knowledge and the resource I used did not make any claim beyond that specific species. Of course, if we find resources that some metabolite (water, phosphate, ions) are found in whole taxa, and that statement can be added at a higher level, and only then can statements for lower taxa be remove, IMHO. At this moment there are very few scholarly resources with machine-readable data that link metabolites with taxa. I love to continue talking. --Egon Willighagen (talk) 08:05, 20 October 2019 (UTC)

"not the task of Wikidata to infer knowledge" I disagree because WD allows such inference as long as it's documented and reproducible. That's why WD has based on heuristic (P887), and you can infer e.g. the gender of Peter Ustinov from the given name if you give based on heuristic (P887)-->inferred from person's given name (Q69652498) as reference. Maybe I should not have said "remove the statements" but better replace by improved statements, and you can do it. You can infer metabolites if you have enzymes that take them as substrate, and get the taxonomic range of the ortholog group of that enzyme. This method in general should get an item, and then you can use it with P887. I know you don't have the time, so I won't waste it further. --SCIdude (talk) 09:47, 20 October 2019 (UTC)

Okay, I think I missed what you want to infer it from. Even for enzymes this is tricky, let alone reactions. Can you give me more detail of the heuristic you have in mind? What would be the (referenced) input data? --Egon Willighagen (talk) 10:26, 26 October 2019 (UTC)

Asking for a letter of support to create a research unit in Tunisia

Dear Sir,

I thank you for your efforts. We are managing to create a research unit called "Data Engineering and Semantics" in the University of Sfax, Tunisia. The purpose of this research unit is to gather Wikiresearchers from University of Sfax into a recognized research structure and have funding from Tunisian Ministry of Higher Education. In order to do that, we need to have a letter of support from institutions all over the world. I ask if you or the director of your research department can write a letter of support for us so that we can have our application approved. This will be acknowledged. --Csisc (talk) 14:27, 23 October 2019 (UTC)

I have never done a LoS for setting up a research group. The information I have so far about the plans are very minimal, and I have zero insight in the community and academic norms the group will uphold. At this moment I will refrain from writing a LoS. Even information about the staff I found hard to find (please provide QIDs and ORCIDs of all staff members). --Egon Willighagen (talk) 10:28, 26 October 2019 (UTC)

opinion needed

Hi Egon, usually I can judge what's right and what's wrong but for this I need confirmation by an expert. This ChEBI entry has a structure of a Vitamin D derivate where the skeleton is different from all related structures I checked---the cyclohexylidene-ethylidene sits on a different position of the 6/5-ring than Vitamin D and derivates. It seems an error, yet they have this structure with name at PubChem and it's our (6R)-6-[(1R,3aS,5Z,7aS)-5-[(2Z)-2-[(5S)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene]-7a-methyl-2,3,3a,4,6,7-hexahydro-1H-inden-1-yl]-2-methylheptane-1,2-diol (Q27161257), that's why I found it. Can you confirm it's wrong (instead of some tautomerism), or do you know someone who can confirm? --SCIdude (talk) 06:57, 1 November 2019 (UTC)

Interesting question, and I do not have a good answer for this at this moment. It's complex. Check this pathway to see some of the chemistry behind Vitamin D. Some of the complexity further originates that, like often in biology, terms are not used consistently. For the particular compound you mention, the name may simply include "vitamin d" in there because it is a breakdown compound of "vitamin D" (many vitamins have a weird compound name history anyway). ChEBI lists an article (PubMed:6286629) that may shed more light and likely will confirm the structure. --Egon Willighagen (talk) 08:29, 1 November 2019 (UTC)

I quickly checked SciFinder and that confirms the structure. --Egon Willighagen (talk) 08:33, 1 November 2019 (UTC)

Open access journals

Thanks for your work on https://blog.ourresearch.org/society-list/ and so many other things! In case you didn't see it, the Wikidata import referenced there is Wikidata_talk:WikiProject_Open_Access#Other_sources_to_import.

I'm currently editing many of the items you created years ago for DOAJ entries. Nemo 09:30, 6 November 2019 (UTC)