#metakids

Sonja 🇳🇱 🇪🇺sonjavan62@mastodon.nl
2025-04-03

Arjen Lubach @arjenlubach doet een veiling voor het goede doel @metakids van de truien met plaatsnamen die hij tijdens zijn laatste theatertour aan had.

metakids.veilet.com/

#Metakids #ArjenLubach #lubach #goeddoel #veiling

2025-01-30

Metakids is het nieuwe officiële goede doel van de Alkmaar City Run by night: tinyurl.com/mu8zmb8j

#hardlopen #alkmaarcityrunbynight #alkmaar #metakids

Egon Willighagenegonw@social.edu.nl
2025-01-06

new blog post: "Serious Request: the results" doi.org/10.59350/fjbv7-53d20

"The last week before the winter break Serious Request took place. We started an action around WikiPathways and we collected 877 euro for the MetaKids Foundation. In total there were 2612 actions, many of which brought in a lot more. We ended up in position 928."

#cheminformatics #bioinformatics #sr24 #metakids #SeriousRequest

Six fragments of a complex biological compound which has the role to anchor proteins in membranes. Several fragments consist of sugar-like rings, where I've been trying to get the stereochemistry right.
Egon Willighagenegonw@social.edu.nl
2024-12-30

it had been a while, but I have updated the curation reports for the #SARSCoV2 / #COVID19 disease maps in @wikipathways: wikipathways.org/SARS-CoV-2-Wi

This include the improvements of the curation stack developed during the recent #SeriousRequest action work for #MetaKids

Laurens 🐐ElBeeToots
2024-12-24

🇳🇱 3FM's Serious Request haalt ruim 11,5 miljoen euro op voor Metakids. Wat een prachtig resultaat! 🥳

Een screenshot van de NOS-website met een foto van de drie 3FM-DJ's uit het Glazen Huis die een bord omhoog houden met daarop het eindbedrag van de actie.
Erik JonkerErikJonker
2024-12-24

Mooie actie weer van , net plaatje aangevraagd en gedoneerd. Doe het nog even !
npo3fm.nl/thema/serious-request
seriousrequest.metakids.nl/

Egon Willigh☮gen 🟥egonw
2024-12-23

Helaas voor mij (maar goed voor ) was de rij heel erg lang, dus ons actie geld inleveren zat er niet in. Doneren aan ons project kan nog steeds! npo3fm.nl/kominactie/acties/wi

Foto van mij voor het gelezen huis in Zwolle. Je kan de dj nog net zien
Linkoramaoffthemarkeet
2024-12-22

Zoooo mn bestelling is geplaatst

Egon Willigh☮gen 🟥egonw
2024-12-22

today I have been working on the reporting, and run the updated curation tests on other sets, e.g. for LIPID MAPS, and the full IEM collection. E.g. more reports in Markdown.

I also worked on the @wdscholia page of Prof. Clara van Karnebeek (orcid:0000-0003-3352-5631), who does not have a Wikipedia page yet (hint, hint). scholia.toolforge.org/author/Q Prof. Karnebeek is one of the people behind MetaKids and has an amazing track record in research into the metabolic disorders.

Egon Willighagenegonw@social.edu.nl
2024-12-22

on one of the last days before the end of #sr24 on national radio, it is getting clear that #metakids is going to get a big donation. The idea that several hundreds of rare metabolic disorders become more treatable in the next 10 years resonates with people. Our own action has now raised 867 euro! npo3fm.nl/kominactie/acties/wi

Thanks to every who donated! Thank you Patrick Luja, thank you Martijn Molenaar!

Screenshot of the linked action page, showing the status bar, with 867 euro of the 1250 euro goal.
Egon Willighagenegonw@social.edu.nl
2024-12-21

find small errors here and there. Today 14 edits in 4 pathways: classic.wikipathways.org/index

1 euro = 1 minute of pathway curation

Help us, help MetaKids, help research into the 1900 deadly inherited metabolic disorders: npo3fm.nl/kominactie/acties/wi

#sr24 #metakids

MediaWiki "recent changes" list for WikiPathways for today, 21 december (winter solstice):

(diff) . . Homo sapiens:Disorders of galactose metabolism : 21 December 2024 by Egonw ‎(galactose translocation)
(diff) . . Homo sapiens:Amino acid metabolism: 21 December 2024 by Egonw ‎(Changed to the ChEBI identifier)
(diff) . . Homo sapiens:Amino acid metabolism: 21 December 2024 by Egonw ‎(Converted labels into data nodes)
(diff) . . Homo sapiens:Amino acid metabolism: 21 December 2024 by Egonw ‎(Converted a metabolite Label to DataNode with identifier)
(diff) . . Mus musculus:Amino acid metabolism: 21 December 2024 by Egonw ‎(Use the ChEBI identifier )
(diff) . . Homo sapiens:Amino acid metabolism: 21 December 2024 by Egonw ‎(The linked ChEBI entry seems to have the correct stereochemistry)
(diff) . . Homo sapiens:Glycosaminoglycan degradation: 21 December 2024 by Egonw ‎(Added a literature reference, about drug targeting)
(diff) . . Homo sapiens:Cytoplasmic ribosomal proteins: 21 December 2024 by Egonw ‎(Oops, wrong species)
(diff) . . Homo sapiens:Cytoplasmic ribosomal proteins: 21 December 2024 by Egonw ‎(Manually set the data source to Complex Portal)
(diff) . . Homo sapiens:Cytoplasmic ribosomal proteins: 21 December 2024 by Egonw ‎(Added a literature reference and Complex Portal identifiers (with wrong datasource))
Egon Willighagenegonw@social.edu.nl
2024-12-21

actually, several more labels in this pathway that should be datanodes

#sr24 #metakids

Screenshot of another section of WP3925 showing four more metabolites that are just labels right now and not DataNode's (circled with red).
Egon Willighagenegonw@social.edu.nl
2024-12-21

another issue that can occur has nothing to do with Wikidata, but is incomplete FAIR-ification of the biological knowledge. We have a test for metabolites that are not involved in an interaction, and I was triggered by the curation test (one of the two screenshots), confirmed in the pathway: a Label needs to be a DataNode.

#sr24 #metakids

Screenshot of the results page of automated curation tests, showing that in WP3925 that OJ-indoleactate and Melanin do not have any interaction: https://www.wikipathways.org/sr24-curation/reports/WP3925#8860e69cSection of WP3925 where we see that OH-indoleacetate is indeed unlinked, because the metabolite it is enzymatically created from is a text label and not a DataNode with identifier.
Egon Willighagenegonw@social.edu.nl
2024-12-21

the Wikidata page we find actually has the HMDB identifier, but deprecated: wikidata.org/wiki/Q2813820

The situation is that HMDB has a different stereoisomer on their page than ChEBI and Wikidata. The latter two have NHNODHRSCRALBF-NQNBQJKNSA-N but HMDB has NHNODHRSCRALBF-XSSXAYJJSA-N

The HMDB team will have to comment on this. When I look at the original pathway and KEGG, I think the ChEBI stated at HMDB is a match with the pathway, so I will fix this by using the ChEBI id 2/2

#sr24 #metakids

Statement for the "Human Metabolite Database ID" HMDB0001157 which has been working on by the Wikidata account Lauraelsevanrooijen1 and AdrianoRutz. They are not wrong.
Egon Willighagenegonw@social.edu.nl
2024-12-21

for example, HMDB0001157 is not found in Wikidata. Looking it up via identifiers.org gives me the record: identifiers.org/hmdb/HMDB00011 goes to hmdb.ca/metabolites/HMDB000115

I confirm the chemical structure with ChEBI, which is listed in HMDB as ebi.ac.uk/chebi/searchId.do?ch

From that page, I take the InChIKey and look it with @wdscholia in @wikidata: scholia.toolforge.org/inchikey 1/

#sr24 #metakids

Egon Willighagenegonw@social.edu.nl
2024-12-21

For example, when @wikipathways has an metabolite identifier we do not have in @wikidata yet, this is a curation signal: did WikiPathways use the wrong identifier (that happens) or is the chemical compound not in Wikidata yet (that happens too). And sometimes something is wrong in Wikidata, like yesterday, when a polymer got accidentally linked to statements about the monomer

The two screenshots show automated curation reports for this for ChEBI and HMDB

#sr24 #MetaKids

Screenshot of the curation page showing that pathways WP3925 and (the new) WP5506 use HMDB identifiers that are not listed in Wikidata.Screenshot of the curation page showing that pathways WP4705, WP4787, WP4815, and WP4917 use ChEBI identifiers that are not listed in Wikidata.
Egon Willighagenegonw@social.edu.nl
2024-12-21

@egonw@mastodon.social so, what role does @wikidata have in our @wikipathways curation?

I think I can break it down into two categories:

1. #Wikidata as hub, linking WikiPathways more tightly into the Linked Open Data network (see link.springer.com/article/10.1)
2. Using @wdscholia to find new, relevant literature to improve the content
3. seed Wikidata with metabolites with little information available about them in public databases

(we have been doing this for years now) 1/

#SR24 #MetaKids

Egon Willigh☮gen 🟥egonw
2024-12-21

thanks to all the positive feedback and donations, we are not stopping with the fundraiser. More curation is happening. I will post a bit about the use of @wikidata in the curation, and meanwhile even further shorten this curation task list: wikipathways.org/sr24-curation

And thank you 22.1 for you donation just now! npo3fm.nl/kominactie/acties/wi

Egon Willighagenegonw@social.edu.nl
2024-12-20

curation is continuing, and if you really want to see what we do, check this feed of #WikiPathways edits: classic.wikipathways.org/index

I am looking into various simpler fixes from this page: wikipathways.org/sr24-curation

Donations are still welcome! We are only at 820 euro now (the full SR24 is at 2.9 million euro for research into inherited metabolic disorders). Help us, help MetaKids, help the kids with metabolic disorders. npo3fm.nl/kominactie/acties/wi

#sr24 #metakids

Screenshot that I shared multiple times now, now saying we raised 820 of 1250 euro.
Egon Willighagenegonw@social.edu.nl
2024-12-20

the fifth day of our NPO 3FM Serious Request action has started. Thanks to everyone who donated money to MetaKids already; the current count is 805 euro for our action for the foundation.

Today, various people (including me) continue to work on the improvement of pathways of metabolic disorders, underlying the number 1 cause of child death in The Netherlands and severe issues otherwise.

#sr24 #metakids

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