new blog post: "Serious Request: the results" https://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

Helaas voor mij (maar goed voor #seriousrequest) was de rij heel erg lang, dus ons actie geld inleveren zat er niet in. Doneren aan ons project kan nog steeds! https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids #sr24 #metakids

Zoooo mn #sr24 #SeriousRequest bestelling is geplaatst #metakids

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). https://scholia.toolforge.org/author/Q56855884 Prof. Karnebeek is one of the people behind MetaKids and has an amazing track record in research into the metabolic disorders.

#sr24 #metakids

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! https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids

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

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

1 euro = 1 minute of pathway curation

Help us, help MetaKids, help research into the 1900 deadly inherited metabolic disorders: https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids

#sr24 #metakids

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

#sr24 #metakids

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

the Wikidata page we find actually has the HMDB identifier, but deprecated: https://www.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

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

I confirm the chemical structure with ChEBI, which is listed in HMDB as http://www.ebi.ac.uk/chebi/searchId.do?chebiId=15476

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

#sr24 #metakids

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

@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 https://link.springer.com/article/10.1186/1758-2946-3-19)
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

thanks to all the positive feedback and donations, we are not stopping with the #SR24 #MetaKids 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: https://www.wikipathways.org/sr24-curation/index2.html

And thank you 22.1 for you donation just now! https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids

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

I am looking into various simpler fixes from this page: https://www.wikipathways.org/sr24-curation/index2.html

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. https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids

#sr24 #metakids

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

@gevoel het is vaak iets van #sr24, weet niet of het dat dit jaar ook is

the day is winding down. we made a lot of progress, in terms of @wikipathways content, but also worked on updating the tooling. First heading home now, get some dinner, and then I see if I can get some more done tonight

#sr24 #metakids

others have been working on more pathways from the book on inherited metabolic disorders, resulting in these two works-in-progress: https://classic.wikipathways.org/instance/WP5506 and https://classic.wikipathways.org/instance/WP5507

You want more of this? Support our fundraiser here: https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids

#sr24 #metakids

@egonw@mastodon.social okay, that should do it. #sr24 #metakids

@egonw@social.edu.nl almost there... meanwhile, making a @bridgedb Java 3.1.14 release for PathVisio, the tool we use to make digital biological pathways in @wikipathways

#sr24 #metakids