#wikipathways — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #wikipathways, aggregated by home.social.
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Important: WikiPathways Technical Transition - Action Required for Some Users
Dear WikiPathways Community,
Effective April 1st, 2026, we will begin taking major steps toward retiring the classic WikiPathways backend as we complete our migration to our GitHub-based infrastructure.
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new blog post: "Where do the WikiPathways come from?" https://chem-bla-ics.linkedchemistry.info/2026/02/22/where-do-the-wikipathways-come-from.html https://doi.org/10.59350/6smn2-ah530
"We can see who the 8 people are who contributed to this pathway [..], and many authors are member of the @wikipathways review team who focus more on technical quality and the biology. The first author, however, often is the person who contributed most of the biological knowledge in the pathway"
Replies to this post show up in the blog.
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WikiPathways RDF IRIs are now dereferenceable! Every http://rdf.wikipathways.org/ identifier now resolves via HTTP with content negotiation: HTML for browsers, Turtle/JSON-LD/RDF-XML/N-Triples for machines.
Try it: click any IRI on the about page, or curl one with an Accept header.
https://rdf.wikipathways.org/about
https://github.com/wikipathways/wikipathways-iri-resolver#LinkedData #FAIR #WikiPathways #RDF #Bioinformatics #SemanticWeb
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hi, if you are using the #WikiPathways (@wikipathways) RDF, please send me a ping. In the coming months, changes are going to happen. To fix and improve some old designs, to add new functionality (like in the January release with more direct IRI links to other knowledge graphs).
Some things may break. And I want to know your use case. I like to get a shortlist of people who I want to give a heads-up and possible even consult on changes in the design and shapes
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"QPX: Pathway analysis environment" https://doi.org/10.37044/osf.io/m37f2_v1
"Building on our work at DBCLS BioHackathon 2023 (BH23), where we introduced QPX and promoted pathway modeling with WikiPathways (Pico et al., 2008) using PathVisio (Kutmon etal., 2015), we now focused on creating new pathway diagrams for diverse species and registering them in WikiPathways with functional annotations. In parallel, we deployed WikiPathways node data into Elasticsearch to enable fast and flexible search and integration of pathway information." https://osf.io/m37f2_v1
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"QPX: Pathway analysis environment" https://doi.org/10.37044/osf.io/m37f2_v1
"Building on our work at DBCLS BioHackathon 2023 (BH23), where we introduced QPX andpromoted pathway modeling with WikiPathways (Pico et al., 2008) using PathVisio (Kutmon etal., 2015), we now focused on creating new pathway diagrams for diverse species and registeringthem in WikiPathways with functional annotations. In parallel, we deployed WikiPathwaysnode data into Elasticsearch to enable fast and flexible search and integration of pathwayinformation." https://doi.org/10.37044/osf.io/m37f2_v1
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"QPX: Pathway analysis environment" https://doi.org/10.37044/osf.io/m37f2_v1
"Building on our work at DBCLS BioHackathon 2023 (BH23), where we introduced QPX and promoted pathway modeling with WikiPathways (Pico et al., 2008) using PathVisio (Kutmon etal., 2015), we now focused on creating new pathway diagrams for diverse species and registering them in WikiPathways with functional annotations. In parallel, we deployed WikiPathways node data into Elasticsearch to enable fast and flexible search and integration of pathway information." https://osf.io/m37f2_v1
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"QPX: Pathway analysis environment" https://doi.org/10.37044/osf.io/m37f2_v1
"Building on our work at DBCLS BioHackathon 2023 (BH23), where we introduced QPX and promoted pathway modeling with WikiPathways (Pico et al., 2008) using PathVisio (Kutmon etal., 2015), we now focused on creating new pathway diagrams for diverse species and registering them in WikiPathways with functional annotations. In parallel, we deployed WikiPathways node data into Elasticsearch to enable fast and flexible search and integration of pathway information." https://osf.io/m37f2_v1
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"QPX: Pathway analysis environment" https://doi.org/10.37044/osf.io/m37f2_v1
"Building on our work at DBCLS BioHackathon 2023 (BH23), where we introduced QPX andpromoted pathway modeling with WikiPathways (Pico et al., 2008) using PathVisio (Kutmon etal., 2015), we now focused on creating new pathway diagrams for diverse species and registeringthem in WikiPathways with functional annotations. In parallel, we deployed WikiPathwaysnode data into Elasticsearch to enable fast and flexible search and integration of pathwayinformation." https://doi.org/10.37044/osf.io/m37f2_v1
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@jerven I had not answered your question yet, and no patch needed, but just to answer it:
1. the original (theseus) code is here: https://github.com/wikipathways/GPML2RDF/tree/main which is used for https://sparql.wikipathways.org/
2. the new libGPML-based code is here: https://github.com/egonw/org.pathvisio.io.rdf which is used for https://plantmetwiki.bioinformatics.nl/
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ah, nice to see the new @Codeberg and @bioconductor features in action! https://research-software-directory.org/software/rwikipathways
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reflecting on my @biocurator Advanced Career Award nomination: "Curation is an essential part of doing research" https://chem-bla-ics.linkedchemistry.info/2025/06/29/curation-is-an-essential-part-of-doing-research.html
replies to this post become blog comments.
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reflecting on my @biocurator Advanced Career Award nomination: "Curation is an essential part of doing research" https://chem-bla-ics.linkedchemistry.info/2025/06/29/curation-is-an-essential-part-of-doing-research.html
replies to this post become blog comments.
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reflecting on my @biocurator Advanced Career Award nomination: "Curation is an essential part of doing research" https://chem-bla-ics.linkedchemistry.info/2025/06/29/curation-is-an-essential-part-of-doing-research.html
replies to this post become blog comments.
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reflecting on my @biocurator Advanced Career Award nomination: "Curation is an essential part of doing research" https://chem-bla-ics.linkedchemistry.info/2025/06/29/curation-is-an-essential-part-of-doing-research.html
replies to this post become blog comments.
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reflecting on my @biocurator Advanced Career Award nomination: "Curation is an essential part of doing research" https://chem-bla-ics.linkedchemistry.info/2025/06/29/curation-is-an-essential-part-of-doing-research.html
replies to this post become blog comments.
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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
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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/113674323267815212Today we have the "WikiPathways in actie voor MetaKids" community day, and now heading to #Maastricht University!
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@[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 :)
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een eerste update. De eerste donaties zijn binnen (dank!).
De planning gaat goed door. Er is een extra persoon aangesloten, de websites zijn wat bijgewerkt, er is een lijst gemaakt met pathways uit een standaardwerk die we kunnen toevoegen, en ik heb de data curatie pijplijn opgezet: https://www.wikipathways.org/sr24-curation/ (die ook de pathways in #SBML vertaalt)
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new blog post: "CiTO updates: Wakefield and WikiPathways" https://chem-bla-ics.linkedchemistry.info/2024/08/07/cito-updates.html
replies to this post become blog comments.
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your ideas about biological processes can be made FAIR in databases like @wikipathways and @reactome
People are using these pathways in their analyses of biological data, and some of those journal articles cite the specific pathways. #WikiPathways makes a reasonable attempt (particularly given the minimal funding) at tracking that.
I just added another three articles, citing some ~20~ish pathways
For example, https://wikipathways.org/instance/WP1601 has been cited at least 4 times
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next week, Denise Slenter will defend her PhD thesis, and in the morning we are organizing a mini symposium With @schymane, @susancoort, Justin van der Hooft, Rachel Cavill, and Laura Steinbusch
If you want to join, you can register here: forms.gle/MsfrRomsiHSk2JPAA #metabolomics #wikipathways #chemistry
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obligatory screenshot, and it's fast indeed #QLever #WikiPathways
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new preprint: "Community curation of kinetic data to support metabolic models through semantic web technology" https://doi.org/10.5281/zenodo.10418717 #wikipathways #rdf #disorders
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De inschrijving voor het VHP4Safety mini-symposium rondom de promotie van Marvin Martens op 29 januari is geopend! https://lnkd.in/dmgHTbUH (Beperkt aantal plaatsen) Met sprekers: Chris Evelo (Marvin's promotor), Holly Mortensen, Anne Kienhuis, Joost Beltman en Mathieu Vinken. #VHP4Safety #AOPWiki #wikipathways
@Marvin's PhD thesis is the result of work in the #OpenRiskNet and #EUToxRisk projects
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online via this live stream tomorrow at 16 CET at https://www.youtube.com/watch?v=PkurGEIOufA #wikipathways #wikidata #shex #textmining
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mark you calendar! "EpiLipidNET Training School: Data Analysis Techniques for preprocessed Lipidomics data" https://www.maastrichtuniversity.nl/events/epilipidnet-training-school-data-analysis-techniques-preprocessed-lipidomics-data #lipidomics #wikipathways #datascience #EpiLipidNet
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Next week Andra Waagmeester (@Andrawaag) will defend his PhD thesis on January 16 on the "Biological Pathway Abstractions: From Two-Dimensional Drawings to Multidimensional Linked Data" (https://www.maastrichtuniversity.nl/events/phd-defence-andra-sachinder-waagmeester). In the morning there will be a mini symposium (see image). Register here today: https://forms.gle/oqMbsVhurBiEQeca7 ! #wikipathways #biology #rdf #wikidata
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okay, the `curl` command is not correct yet (after shopping/dinner), but the "Run" and "Edit" links are now working for all SPARQL endpoints :) https://bigcat-um.github.io/PRA3006-SPARQL/wikipathways.html #wikidata #wikipathways #chembl #AOPWiki
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okay, the `curl` command is not correct yet (after shopping/dinner), but the "Run" and "Edit" links are now working for all SPARQL endpoints :) https://bigcat-um.github.io/PRA3006-SPARQL/wikipathways.html #wikidata #wikipathways #chembl #AOPWiki
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okay, the `curl` command is not correct yet (after shopping/dinner), but the "Run" and "Edit" links are now working for all SPARQL endpoints :) https://bigcat-um.github.io/PRA3006-SPARQL/wikipathways.html #wikidata #wikipathways #chembl #AOPWiki
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okay, the `curl` command is not correct yet (after shopping/dinner), but the "Run" and "Edit" links are now working for all SPARQL endpoints :) https://bigcat-um.github.io/PRA3006-SPARQL/wikipathways.html #wikidata #wikipathways #chembl #AOPWiki
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okay, the `curl` command is not correct yet (after shopping/dinner), but the "Run" and "Edit" links are now working for all SPARQL endpoints :) https://bigcat-um.github.io/PRA3006-SPARQL/wikipathways.html #wikidata #wikipathways #chembl #AOPWiki