Milestone! "To date, 902 pathways have been cited a total of 3018 times" https://www.wikipathways.org/browse/citedin.html #biology #openscience

Milestone! "To date, 902 pathways have been cited a total of 3018 times" https://www.wikipathways.org/browse/citedin.html #biology #openscience

@Marvin upgraded our SPARQL interface. It now show a title and a description, and making it easier to navigate the example queries: https://sparql.wikipathways.org/ (maybe do a hard reload) #openscience #bioinformatics

hi all, as promised (and really no joke), we are today shutting down the Classic website. Step 1: take the webservice offline (done)

hi, scrapers have been crawling the classic website for more than half a year now. We are trying to keep it at manageable levels, but our options are running out. So, right now, we had to enable the "under attack" mode of @cloudflare This likely breaks the webservice... but we first need to […]

March 2026 WikiPathways update: 45 edits by 5 contributors in the last month. More news at https://github.com/wikipathways/wikipathways-help/discussions/227 Accessible via #webservices, #rstats, #PathVisio and #Cytoscape. Supported by #AWSOpen […]

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. 1/ […]

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. 1/ […]

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 […] [Original post on social.edu.nl]

Dear WikiPathways #community, We want to share an important update about our WikiPathways leadership. ✨After nearly 20 years of dedication since co-founding WikiPathways in 2007, the Gladstone team, including Alexander Pico and Kristina Hanspers, are transitioning away from their leadership […]

February 2026 WikiPathways update: 95 edits by 9 contributorsin the last month. More news at https://github.com/wikipathways/wikipathways-help/discussions/221 Accessible via #webservices, #rstats, #PathVisio and #Cytoscape. Supported by #AWSOpen […]

hi, if you are using the #WikiPathways (@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 […]

January 2026 WikiPathways update: 134 edits by 3 contributorsin the last month. More news at https://github.com/wikipathways/wikipathways-help/discussions/213 Accessible via #webservices, #rstats, #PathVisio and #Cytoscape. Supported by #AWSOpen […]

"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 […] [Original post on fediscience.org]

December 2025 WikiPathways release: 840 edits by 8 contributors and 9 new pathways. Accessible via #webservices, #rstats, #PathVisio and #Cytoscape. https://www.wikipathways.org/#download #bioinformatics #elixirnl

new paper describing 5 #cakut pathways, WP4823, WP4830, WP5052, WP5053, and WP5236: "Here, we develop and describe fully machine-readable, well-annotated pathways to visualize and analyze key events during kidney development." https://doi.org/10.1016/j.kint.2025.09.032

@wikipathways @egonw Next attempt. Just using these libs: library(rWikiPathways) library(XML) library(dplyr) library(igraph) library(ggraph) library(ggplot2) Still need to polish and work on the colour scale, though. Honestly? I, considering my workload, I […] [Original post on fediscience.org]

got GPML files on @github? Validate them with this action: jobs: test: name: "Validate XSD files" runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@v6 - name: Validate XSD files conform to the specs uses: phpcsstandards/xmllint-validate@v1 with: pattern: "pathways/*.gpml" […]

@egonw a few days ago, I updated bumped the #Bioconda package of r-wikipathways to v1.30 . Thank you for this wonderful package! Today, after quite some tinkering, I managed to overly differential expression results. This is not stable code, yet. The […] [Original post on fediscience.org]

November’s #LipidoftheMonth is a rare phospholipid with links to ferroptosis lipidmaps.org/updates/lipi...

hi all, as you may have heard elsewhere, @cloudflare has having some struggling. this affects our websites too. you can monitor their work to restore their status here: https://www.cloudflarestatus.com/

Hi everyone, we have updated the author and community pages on our website. Authors can now find curation reports for pathways they started, and Communities can find those too. We hope you like it! https://github.com/wikipathways/wikipathways-help/discussions/203 #openscience #biology #biocuration

Hi everyone, we have updated the author and community pages on our website. Authors can now find curation reports for pathways they started, and Communities can find those too. We hope you like it! https://github.com/wikipathways/wikipathways-help/discussions/203 #openscience #biology #biocuration

November 2025 WikiPathways update: 686 edits by 6 contributors and 10 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

just minting some protein identifiers in #wikidata, so that I can link them to literature, and thus enriching @wikipathways#wikidata qid,P31,P703,Len,Den ,Q8054,Q209089,"""PcCS1""","""guarana protein""" ,Q8054,Q209089,"""PcCS1""","""guarana protein""" ,Q8054,Q209089,"""PcCS""","""guarana protein"""

five new species, five new pathways, five ways caffeine is synthesized: - Theobroma cacao caffeine synthesis (WP5588): https://www.wikipathways.org/pathways/WP5588.html - Citrus sinensis caffeine synthesis (WP5589) […] [Original post on fosstodon.org]

hi all, the domain name is being transferred and the website may not be accessible right now. Hopefully this is solved soon!

October 2025 WikiPathways update: 129 edits by 10 contributors and 5 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 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