The rise of ADP-ribose–ubiquitin Ok, this has gone too far. A PTM on a PTM on a PTM on a PTM... https://www.nature.com/articles/s41594-025-01651-0

September 2025 WikiPathways update: 261 edits by 6 contributors and 13 new pathways in the last month. Accessible via #webservices, #rstats, #PathVisio and #Cytoscape. Supported by #AWSOpen. https://www.wikipathways.org/index.php/Download_Pathways #bioinformatics #openscience #opensource

the new @wikipathways RDF is loaded in the SPARQL endpoint and this includes triples we did not have before, based on the "Cited In" functionality of WikiPathways (see https://fosstodon.org/@wikipathways/114925438577051352). So, you can now list all pathways […] [Original post on social.edu.nl]

August 2025 WikiPathways release: 367 edits by 10 contributors and 26 new pathways. https://data.wikipathways.org/ #openscience #biology #pfas

things I am doing this morning: 1. check up on the impact of retracted articles (with @wikidata) 2. curation of @wikipathways pathways The second follows up from work yesterday, going through a long list of pathways on the old website but not on the new […] [Original post on mastodon.social]

"We utilized a #python script with the xml.etree.ElementTree parser module to analyze the WP2877 GPML file from WikiPathways. This script focused on ‘DataNode’ elements to extract the ‘TextLabel’ attribute, assembling a comprehensive list of genes essential to the VDR pathway. After removing […]

New release of PFOCR! Over 6,500 new pathway figures added for a total of 116,972. These include 147,974 unique genes across hundreds of species (18,775 human), 7,855 unique ChEBI, and 748 unique disease DOIDs. https://pfocr.wikipathways.org Using the search […] [Original post on fosstodon.org]

For almost 2 years we have been tracking which literature for citations to specific pathways, via their WikiPathways WPID. Results are shown on pathway pages, under "Cited in", e.g. see https://www.wikipathways.org/pathways/WP3947 (and screenshot). This is […] [Original post on fosstodon.org]

July 2025 WikiPathways release: 531 edits by 15 contributors and 2 new pathways. https://data.wikipathways.org/ #openscience #biology #RareDisease

if you are using our old webservice API and experienced problems in the past few weeks, please email us to help you migrate to the new API or ask at https://github.com/wikipathways/wikipathways-help/discussions

June 2025 WikiPathways release: 338 edits by 15 contributors and 9 new pathways. https://data.wikipathways.org/ Accessible via #webservices, #rstats, Pathvisio, and Cytoscape.

May 2025 WikiPathways release: 491 edits by 9 contributors and 8 new pathways. Accessible via #webservices, #rstats, Pathvisio, and Cytoscape. #biology #bioinformatics

"Diseae Ontology]’s FAIR-ness has further been strengthened by revamping the REST API, reorganizing and expanding the SPARQL queries provided with DO-KB’s SPARQL Sandbox, particularly the federated queries that access multiple endpoints to interconnect data (e.g., WikiPathways, MeSH), and […]

upcoming online workshop, 2x 2 hours, by the ERDERA project, on Rare Disease Maps, May 6 and 7 from 3-5pm CEST: "Rare Disease Maps" Day 1: https://events.teams.microsoft.com/event/009dccd2-5c8f-465e-ad28-15056854f2e4@b89cc6a7-57a7-4137-8224-69e7ea0b1c55 Day 2 […] [Original post on fosstodon.org]

@bioconductor 3.21 is out, including rWikiPathways 1.28: https://bioconductor.org/packages/release/bioc/html/rWikiPathways.html See https://genomic.social/@bioconductor/114349555185162646 for the general announcement

:mega: April 2025 WikiPathways release: 454 edits by 10 contributors and 9 new pathways. Accessible via #webservices, #rstats, Pathvisio, and Cytoscape. Supported by AWSOpen https://www.wikipathways.org/download.html #biology #bioinformatics #openscience

very exciting Google Summer of Code project idea around @wikipathways for a great student with a lot of enthusiasm and drive to learn a lot of new things and get things done! https://github.com/nrnb/GoogleSummerOfCode/issues/264 #bioinformatics #openscience

March 2025 WikiPathways release: 1,297 edits by 6 contributors and 1 new pathway Accessible via #webservices, #rstats, Pathvisio, and Cytoscape. Supported by AWSOpen https://www.wikipathways.org/download.html #biology #crohn #bioinformatics #openscience

Februari 2025 WikiPathways update: 313 edits by 10 contributors and 4 new pathways in the last month. Accessible via #webservices, #rstats, Pathvisio, and Cytoscape. Supported by AWSOpen https://www.wikipathways.org/download.html #biology #bioinformatics #openscience

January 2025 WikiPathways update: 154 edits by 11 contributors and 5 new pathways in the last month. Accessible via #webservices, #rstats, Pathvisio, and Cytoscape. Supported by AWSOpen https://wikipathways.org/index.php/Download_Pathways #bioinformatics #openscience #opensource

hi @rhea-db.bsky.social !

December 2024 WikiPathways update: 272 edits by 7 contributors and 11 new pathways in the last month. Accessible via #webservices, #rstats, Pathvisio, and Cytoscape. Supported by AWSOpen. https://wikipathways.org/index.php/Download_Pathways #bioinformatics #openscience #opensource

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 […] [Original post on social.edu.nl]

actually, several more labels in this pathway that should be datanodes #sr24 #metakids

the Serious Request fundraiser is nearing. The DJs lock themselves up in just under two weeks and on the 16th I start a week long working on metabolic disease related pathways, joined by already three others: https://sr24.wikipathways.org/ But the preparation […] [Original post on social.edu.nl]

now that the WikiPathways team at Maastricht University (UM) is distributed over more than one department, it was time for a "UM WikiPathways" day. Martina Kutmon organized the first meeting, and wrote up a short post about it […]

our pathways have been associated with more than 500 diseases. https://edu.nl/rj6jm Cancer and SARS have (currently) the most pathways linked to them. #biology #disease #sparql