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#Metakids

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Egon Willighagen<p>new blog post: "Serious Request: the results" <a href="https://doi.org/10.59350/fjbv7-53d20" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">doi.org/10.59350/fjbv7-53d20</span><span class="invisible"></span></a></p><p>"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."</p><p>replies to this post become blog comments.</p><p><a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> <a href="https://social.edu.nl/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://social.edu.nl/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://social.edu.nl/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a> <a href="https://social.edu.nl/tags/SeriousRequest" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SeriousRequest</span></a></p>
Egon Willighagen<p>it had been a while, but I have updated the curation reports for the <a href="https://social.edu.nl/tags/SARSCoV2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SARSCoV2</span></a> / <a href="https://social.edu.nl/tags/COVID19" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>COVID19</span></a> disease maps in <span class="h-card" translate="no"><a href="https://fosstodon.org/@wikipathways" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wikipathways</span></a></span>: <a href="https://www.wikipathways.org/SARS-CoV-2-WikiPathways/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">wikipathways.org/SARS-CoV-2-Wi</span><span class="invisible">kiPathways/</span></a></p><p>This include the improvements of the curation stack developed during the recent <a href="https://social.edu.nl/tags/SeriousRequest" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SeriousRequest</span></a> action work for <a href="https://social.edu.nl/tags/MetaKids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MetaKids</span></a></p>
Erik Jonker<p>Mooie actie weer van <a href="https://mastodon.social/tags/3FM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>3FM</span></a> <a href="https://mastodon.social/tags/SeriousRequest" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SeriousRequest</span></a> , net plaatje aangevraagd en gedoneerd. Doe het nog even !<br><a href="https://www.npo3fm.nl/thema/serious-request" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="">npo3fm.nl/thema/serious-request</span><span class="invisible"></span></a><br><a href="https://seriousrequest.metakids.nl/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">seriousrequest.metakids.nl/</span><span class="invisible"></span></a><br><a href="https://mastodon.social/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
Egon Willigh☮gen 🟥<p>Helaas voor mij (maar goed voor <a href="https://mastodon.social/tags/seriousrequest" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>seriousrequest</span></a>) was de rij heel erg lang, dus ons actie geld inleveren zat er niet in. Doneren aan ons project kan nog steeds! <a href="https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">npo3fm.nl/kominactie/acties/wi</span><span class="invisible">kipathways-in-actie-voor-metakids</span></a> <a href="https://mastodon.social/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://mastodon.social/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
Egon Willigh☮gen 🟥<p>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.</p><p>I also worked on the <span class="h-card" translate="no"><a href="https://wikis.world/@wdscholia" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wdscholia</span></a></span> page of Prof. Clara van Karnebeek (orcid:0000-0003-3352-5631), who does not have a Wikipedia page yet (hint, hint). <a href="https://scholia.toolforge.org/author/Q56855884" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">scholia.toolforge.org/author/Q</span><span class="invisible">56855884</span></a> Prof. Karnebeek is one of the people behind MetaKids and has an amazing track record in research into the metabolic disorders.</p><p><a href="https://mastodon.social/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://mastodon.social/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
Egon Willighagen<p>on one of the last days before the end of <a href="https://social.edu.nl/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> on national radio, it is getting clear that <a href="https://social.edu.nl/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a> 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! <a href="https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">npo3fm.nl/kominactie/acties/wi</span><span class="invisible">kipathways-in-actie-voor-metakids</span></a></p><p>Thanks to every who donated! Thank you Patrick Luja, thank you Martijn Molenaar!</p>
Egon Willighagen<p>find small errors here and there. Today 14 edits in 4 pathways: <a href="https://classic.wikipathways.org/index.php/Special:RecentPathwayChanges" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">classic.wikipathways.org/index</span><span class="invisible">.php/Special:RecentPathwayChanges</span></a></p><p>1 euro = 1 minute of pathway curation</p><p>Help us, help MetaKids, help research into the 1900 deadly inherited metabolic disorders: <a href="https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">npo3fm.nl/kominactie/acties/wi</span><span class="invisible">kipathways-in-actie-voor-metakids</span></a></p><p><a href="https://social.edu.nl/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://social.edu.nl/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
Egon Willighagen<p>actually, several more labels in this pathway that should be datanodes</p><p><a href="https://social.edu.nl/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://social.edu.nl/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
Egon Willighagen<p>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.</p><p><a href="https://social.edu.nl/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://social.edu.nl/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
Egon Willighagen<p>the Wikidata page we find actually has the HMDB identifier, but deprecated: <a href="https://www.wikidata.org/wiki/Q2813820" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="">wikidata.org/wiki/Q2813820</span><span class="invisible"></span></a></p><p>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</p><p>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</p><p><a href="https://social.edu.nl/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://social.edu.nl/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
Egon Willighagen<p>for example, HMDB0001157 is not found in Wikidata. Looking it up via identifiers.org gives me the record: <a href="https://identifiers.org/hmdb/HMDB0001157" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">identifiers.org/hmdb/HMDB00011</span><span class="invisible">57</span></a> goes to <a href="https://hmdb.ca/metabolites/HMDB0001157" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">hmdb.ca/metabolites/HMDB000115</span><span class="invisible">7</span></a></p><p>I confirm the chemical structure with ChEBI, which is listed in HMDB as <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=15476" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">http://www.</span><span class="ellipsis">ebi.ac.uk/chebi/searchId.do?ch</span><span class="invisible">ebiId=15476</span></a></p><p>From that page, I take the InChIKey and look it with <span class="h-card" translate="no"><a href="https://wikis.world/@wdscholia" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wdscholia</span></a></span> in @wikidata: <a href="https://scholia.toolforge.org/inchikey/NHNODHRSCRALBF-NQNBQJKNSA-N" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">scholia.toolforge.org/inchikey</span><span class="invisible">/NHNODHRSCRALBF-NQNBQJKNSA-N</span></a> 1/</p><p><a href="https://social.edu.nl/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://social.edu.nl/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
Egon Willighagen<p>For example, when <span class="h-card" translate="no"><a href="https://fosstodon.org/@wikipathways" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wikipathways</span></a></span> has an metabolite identifier we do not have in <span class="h-card" translate="no"><a href="https://wikis.world/@wikidata" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wikidata</span></a></span> 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</p><p>The two screenshots show automated curation reports for this for ChEBI and HMDB</p><p><a href="https://social.edu.nl/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://social.edu.nl/tags/MetaKids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MetaKids</span></a></p>
Egon Willighagen<p><span class="h-card" translate="no"><a href="https://mastodon.social/@egonw" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>egonw@mastodon.social</span></a></span> so, what role does <span class="h-card" translate="no"><a href="https://wikis.world/@wikidata" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wikidata</span></a></span> have in our <span class="h-card" translate="no"><a href="https://fosstodon.org/@wikipathways" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wikipathways</span></a></span> curation?</p><p>I think I can break it down into two categories:</p><p>1. <a href="https://social.edu.nl/tags/Wikidata" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Wikidata</span></a> as hub, linking WikiPathways more tightly into the Linked Open Data network (see <a href="https://link.springer.com/article/10.1186/1758-2946-3-19" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">link.springer.com/article/10.1</span><span class="invisible">186/1758-2946-3-19</span></a>)<br>2. Using <span class="h-card" translate="no"><a href="https://wikis.world/@wdscholia" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wdscholia</span></a></span> to find new, relevant literature to improve the content<br>3. seed Wikidata with metabolites with little information available about them in public databases</p><p>(we have been doing this for years now) 1/</p><p><a href="https://social.edu.nl/tags/SR24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SR24</span></a> <a href="https://social.edu.nl/tags/MetaKids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MetaKids</span></a></p>
Egon Willigh☮gen 🟥<p>thanks to all the positive feedback and donations, we are not stopping with the <a href="https://mastodon.social/tags/SR24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SR24</span></a> <a href="https://mastodon.social/tags/MetaKids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MetaKids</span></a> fundraiser. More curation is happening. I will post a bit about the use of <span class="h-card" translate="no"><a href="https://wikis.world/@wikidata" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wikidata</span></a></span> in the curation, and meanwhile even further shorten this curation task list: <a href="https://www.wikipathways.org/sr24-curation/index2.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">wikipathways.org/sr24-curation</span><span class="invisible">/index2.html</span></a></p><p>And thank you 22.1 for you donation just now! <a href="https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">npo3fm.nl/kominactie/acties/wi</span><span class="invisible">kipathways-in-actie-voor-metakids</span></a></p>
Egon Willighagen<p>curation is continuing, and if you really want to see what we do, check this feed of <a href="https://social.edu.nl/tags/WikiPathways" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>WikiPathways</span></a> edits: <a href="https://classic.wikipathways.org/index.php/Special:RecentPathwayChanges" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">classic.wikipathways.org/index</span><span class="invisible">.php/Special:RecentPathwayChanges</span></a></p><p>I am looking into various simpler fixes from this page: <a href="https://www.wikipathways.org/sr24-curation/index2.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">wikipathways.org/sr24-curation</span><span class="invisible">/index2.html</span></a></p><p>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. <a href="https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">npo3fm.nl/kominactie/acties/wi</span><span class="invisible">kipathways-in-actie-voor-metakids</span></a></p><p><a href="https://social.edu.nl/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://social.edu.nl/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
Egon Willighagen<p>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.</p><p>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.</p><p><a href="https://social.edu.nl/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://social.edu.nl/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
Marion<p><span class="h-card" translate="no"><a href="https://mastodon.nl/@NunlRSS" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>NunlRSS</span></a></span> kijk “voor de volgende Jelte” op npo3 <a href="https://mastodon.nl/tags/BNNVARA" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>BNNVARA</span></a> terug, dan weet je wat een metabole ziekte is en waar deze actie over gaat ! En dus weet je waarom je moet doneren <a href="https://mastodon.nl/tags/Seriousrequest" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Seriousrequest</span></a> <a href="https://mastodon.nl/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
Egon Willighagen<p>the day is winding down. we made a lot of progress, in terms of <span class="h-card" translate="no"><a href="https://fosstodon.org/@wikipathways" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wikipathways</span></a></span> 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</p><p><a href="https://social.edu.nl/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://social.edu.nl/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
Egon Willighagen<p>others have been working on more pathways from the book on inherited metabolic disorders, resulting in these two works-in-progress: <a href="https://classic.wikipathways.org/instance/WP5506" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">classic.wikipathways.org/insta</span><span class="invisible">nce/WP5506</span></a> and <a href="https://classic.wikipathways.org/instance/WP5507" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">classic.wikipathways.org/insta</span><span class="invisible">nce/WP5507</span></a></p><p>You want more of this? Support our fundraiser here: <a href="https://www.npo3fm.nl/kominactie/acties/wikipathways-in-actie-voor-metakids" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">npo3fm.nl/kominactie/acties/wi</span><span class="invisible">kipathways-in-actie-voor-metakids</span></a></p><p><a href="https://social.edu.nl/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://social.edu.nl/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
Egon Willighagen<p><span class="h-card" translate="no"><a href="https://mastodon.social/@egonw" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>egonw@mastodon.social</span></a></span> okay, that should do it. <a href="https://social.edu.nl/tags/sr24" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sr24</span></a> <a href="https://social.edu.nl/tags/metakids" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metakids</span></a></p>
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