#metakids — Public Fediverse posts

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."

replies to this post become blog comments.

#cheminformatics #bioinformatics #sr24 #metakids #SeriousRequest

Mooie actie weer van #3FM #SeriousRequest , net plaatje aangevraagd en gedoneerd. Doe het nog even !
https://www.npo3fm.nl/thema/serious-request
https://seriousrequest.metakids.nl/
#metakids

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

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

@[email protected] 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

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

@[email protected] okay, that should do it. #sr24 #metakids

@[email protected] 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

@[email protected] fixing the last bits of stereochemistry...

meanwhile, thank you Sanne and Unnamed for your donations! We are at 750 euro now :)

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

#sr24 #MetaKids

next update, more rings and piecing things together #sr24 #metakids

okay, I think I have the first ring (was distracted with a few other tasks in the action): https://cdkdepict.cloud.vhp4safety.nl/depict/bot/svg?smi=POC%5BC%40%40H%5D1%5BC%40%40H%5D(O)%5BC%40H%5D(%5BR11%5D)%5BC%40H%5D(%5BR10%5D)C(O1)O%5BM%5D&w=-1&h=-1&abbr=on&hdisp=bridgehead&showtitle=false&zoom=1.25&annotate=cip&r=0

Next ring...

#sr24 #metakids

@[email protected] thank you Nomi, thank you Fien, for your donations to #MetaKids!

We are at 750 euro now with our @wikipathways action for MetaKids!

I am here now with Denise and Daan, and Marek and Tina will join todays #sr24 hackathon.

How you can help:
- donate to MetaKids: https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids
- raise awareness on your social channels about these life-threatening metabolic disorders
- request your research paper to be added to @wikipathways: https://mastodon.social/@egonw/113674994239682083

meanwhile, one @bridgedb feature request implemented: the website now also lists the species common names (if giving on the JSON config files)

#sr24 #metakids #ELIXIREurope

going to try to make this chemical structure FAIR ...

That should be worth 5 euro for the MetaKids foundation, not? Donate to this charity here: https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids

#sr24 #metakids #chemistry #cheminformatics

this is the fourth day of the Serious Request fundraising for #MetaKids of our #WikIPathways action. The DJs locked themselves up in the glass house in the Overijssel city Zwolle yesterday afternoon, the our @wikipathways now raised 730 euro :)

Highlights yesterday include:

- https://mastodon.social/@egonw/113674994239682083
- https://mastodon.social/@egonw/113674323267815212

Today we have the "WikiPathways in actie voor MetaKids" community day, and now heading to #Maastricht University!

#sr24 #metakids

if you have studied any of the genes or metabolites in these 34 pathways, donate 5 euro with the HGNC code or InChIKey of the metabolite and the DOI of the article at https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids

And then I will do my best to use the reference to back up the pathway. Detailed explanation as reply here is most welcome, of course!

#sr24 #metakids #metabolomics #genomics #openscience

updated the curation tests, and the new results for the #SR24 #Metakids focus set are updated (slightly lower than before)

Mind you, these tests are tough. E.g. it expects that every interaction has at least on reference that supports that interaction. It's not easy to meet that expectation, but the curators are doing their best

@[email protected] only 15 euro, three small donations, away from the 600 euro milestone :) https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids

This puts us at place 689 (page 58) in the lists of projects bringing in the most funding for Metakids: https://www.npo3fm.nl/kominactie/acties?sort=collected_amount&page=58

#sr24 #metakids

Day three of our Serious Request fundraiser activity has started.

Plans for me for today: start pathway for second focus article, add information to existing pathways. References per (biological) interaction sounds good, but not trivial. A lot of literature has data from model systems, which is in the narrative then "translated" to human.

#sr24 #metakids

@[email protected] meanwhile making good progress on this Glycosylphosphatidyl inositol anchor pathway from https://doi.org/10.1016/j.ymgme.2015.04.007 for @wikipathways :) It has multiple genes new to WikiPathways, including PIGS and who doesn't like PIGS? Right? https://classic.wikipathways.org/index.php/Pathway:WP5505

If you like #PIGS too, help us, help MetaKids, help the kids with metabolic disorders.

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

#sr24 #metakids

@[email protected] een tweede update. om het makkelijker te maken om prioriteiten te stellen, zijn de curatie testen nu niet meer rood of groen, maar ook geel en oranje, afhankelijk van hoeveel er aan het pathway te verbeteren valt :)

#SR24 #WikiPathways #MetaKids