WikiPathways

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/ […]

Screenshot from the blog post, showing the WikiPathways SPARQL interface with a SPARQL query in the text box in the top left, on the right hand side a folder structure with other examples SPARQL queries, and in the bottom a table with results from the text box SPARQL query. The table shows a list of eight authors of the pathways with identifier WP10. It shows their names, there profile pages, and for some of them, their ORCID identifiers.

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]

📢 We are excited about the future of WikiPathways and grateful for your continued support and contributions. Stay tuned for upcoming announcements about important technical developments as we continue to evolve the platform.

Don't hesitate to reach out if you have any questions, want to get […]

WikiPathways will continue under the leadership of Martina Summer-Kutmon and Egon Willighagen. Both have been deeply involved with WikiPathways for over a decade and have been in leadership roles for many years, working alongside Alex to develop and maintain the platform. Together with our […]

His contributions to #pathway #curation, #openscience, and the broader #bioinformatics community have left a lasting impact, and we are grateful for everything he has built with this project. Kristina has coordinated our curation efforts from the very beginning, and we are happy that she will […]

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) 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 […]

Screenshot of the linked BioHackrXiv preprint, showing the top half of a preprint PDF page, showing the BioHackrXiv logo from the template, a table at the top listing a Arabidopsis thaliana pathway, and below that part of Figure 1 showing a "[p]athway diagram for for Caffeine synthesis inCoffea arabica. This diagram is already published in WikiPathways at https://www.wikipathways.org/pathways/WP5586.html".

"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]

WikiPathways WP5609: Key metabolic pathways in melanoma, glycolytic pathway, TCA cycle, glutamine metabolism, and oxidative phosphorylation, with potential therapeutic targets and inhibitors. Inhibitors targeting critical metabolic nodes are outlined in teal. This pathway is based on Figure 1 in Shen et al.

WikiPathways WP5606: Cis- and trans-acting regulators shape gene expression within the β-globin cluster. The LDB1 complex (LDB1/LMO2/GATA1/TAL1) binds both the locus control region (LCR) and globin promoters, promoting chromatin looping to activate these genes—interactions that may be influenced by cis-acting variants linked to HbS haplotypes. Across the HBB gene cluster and its surrounding regions, BCL11A and ZBTB7A (LRF) binding sites are present, represented by red and blue stars. Each of these transcription factors recruits its own NuRD complex. MYB regulates HbF expression directly and also indirectly through KLF1 and BCL11A. Repression of the HbF genes is indicated by dashed lines. Inspired by figure 1 in Habara et al. (2017).

WikiPathways WP5604: This pathway shows the molecular pathophysiology of sickle cell disease. (A) A single–nucleotide variant in the β-globin gene replaces glutamic acid with valine at position 6 of the β-globin chain. Upon deoxygenation, the resulting hemoglobin S (HbS) molecules polymerize into rigid fibers, driving erythrocyte sickling (clockwise). (B) Sickled cells cause impaired blood rheology and enhanced adhesion of erythrocytes to neutrophils, platelets, and the endothelium, leading to slowed or obstructed microvascular flow – called vaso-occlusion. Vaso-occlusion in turn promotes ischemia-reperfusion (I-R) injury (clockwise). (C) HbS polymer formation also leads to red cell membrane damage and hemolysis (counterclockwise), releasing cell-free hemoglobin (Hb) into circulation. Oxygenated Hb (Fe²⁺) contributes to endothelial dysfunction by consuming nitric oxide (NO) and producing nitrate (NO₃⁻) and methemoglobin (Fe³⁺). Hb can also undergo Fenton chemistry with H₂O₂, generating hydroxyl radicals (•OH) and additional methemoglobin. Methemoglobin (Fe³⁺) can degrade and release cell-free heme (counterclockwise), a potent erythrocyte-derived DAMP. (D) ROS production, TLR4 activation, NET formation, release of tissue- or cell-derived DAMPs, extracellular DNA, and other yet-undefined mediators generated by cell-free heme or I-R injury can induce sterile inflammation by activating the inflammasome in vascular and immune cells, leading to IL-1β release.

WikiPathways WP5607: Erythroid lineage cell differentiation transitions from hematopoietic stem cells (HSCs) through successive erythroid progenitors – burst-forming unit–erythroid (BFU-E), colony-forming unit–erythroid (CFU-E) – then proerythroblasts (proEB), basophilic erythroblasts (basoEB), polychromatic erythroblasts (polyEB), and orthochromatic erythroblasts (orthoEB), then and ultimately to reticulocytes, pyrenocytes, and mature red blood cells (RBCs). Stage-specific transcription factors (GATA1, GATA2), surface markers (CD34, CD45, CD71, CD235a), the onset of hemoglobin expression, and other factors are also depicted.

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

Figure 3. Subnetworks derived from kidney development pathways, extended with chemical compound information and annotated with the compounds’ usages in humans. (a) Subnetwork showing interactions of known nephrotoxic compounds with kidney development pathway proteins. (b) Herbicidal compounds interacting with kidney development pathway proteins. (c) Chemical compounds binding to or affecting expression of GDNF. AMP, adenosine monophosphate.

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

overlay plot of a wikipathway showing over- and under expressed genes in red, resp. blue.

@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" […]

@rupdecat @egonw please create a PR for this page to link to your package: https://www.wikipathways.org/download.html

Result of an R-Script illustrating downregulation (shades of blue) in a Drosophila pathway. The dataset was small, the results not reliable, the biological interpretation not feasible.

@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...

Cloudflare Status Welcome to Cloudflare's home for real-time and historical data on system performance.

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/

Screenshot of the COVID-19 Community page with the pathways curated by this community, showing thumbnails of 21 pathways along with full title and a curation report badge showing the number of curation events. These are colored by the number of events, mostly yellow (1-2 suggestions) and orange (3-4 suggestions) here.

Screenshot of Europe PMC for pathways of the COVID-19 Community page. It shows a few relevant journal articles mentioning specific COVID-19 pathways.

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

Screenshot of the COVID-19 Community page with the pathways curated by this community, showing thumbnails of 21 pathways along with full title and a curation report badge showing the number of curation events. These are colored by the number of events, mostly yellow (1-2 suggestions) and orange (3-4 suggestions) here.

Screenshot of Europe PMC for pathways of the COVID-19 Community page. It shows a few relevant journal articles mentioning specific COVID-19 pathways.

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

New pathway, Caffeine in blood vessels (WP5601). In vascular smooth muscle, caffeine promotes relaxation by inhibiting myosin light-chain kinase (MLCK) through cAMP elevation and activating myosin light-chain phosphatase (MLCP), reducing myosin–actin interaction. As a nonselective adenosine receptor antagonist, caffeine blocks A₁/A₃ receptors (which normally lower cAMP) and A₂A/A₂B receptors (which normally raise cAMP), thereby altering adenylate cyclase activity. In endothelial cells, caffeine increases intracellular Ca²⁺, activating eNOS to produce nitric oxide (NO), which diffuses to smooth muscle and stimulates cGMP signaling, further promoting vasodilation. Inspired by Figure 1 in Kumar and Lipshultz, 2019.

New pathway, KCNQ2 and KCNQ3-related epilepsy (WP5599): Processes involved in KCNQ2 and KCNQ3-related epilepsies.

New pathways, GABA and glutamate signalling in epileptogenesis (WP5600): This pathway depicts the epileptogenic mechanisms involving GABA and glutamate signaling. It focuses on transporters and channel proteins that modulate action potential dynamics and their interacting partners, highlighting functional alterations that contribute to epilepsy pathogenesis.

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

qid,P31,P703,Len,Den
,Q8054,Q209089,"""PcCS1""","""guarana protein"""
,Q8054,Q209089,"""PcCS1""","""guarana protein"""
,Q8054,Q209089,"""PcCS""","""guarana protein"""

Depiction of the caffeine synthesis pathway in Coffea arabica showing a 6-step biosynthesis starting with xanthosine monophosphate, involving 5 proteins.

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]

all (sub)domains should be back. Make sure to use www.wikipathways.org as wikipathways.org (without the www) is the last hurdle

okay, www.wikipathways.org is back and several other subdomains too. The others will follow tomorrow, but if you need a subdomain urgently, please ping @egonw

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 - Nature Structural & Molecular Biology Post-translational modifications show mechanistic crosstalk, exemplified by the ADP-ribose–ubiquitin hybrid signal, in which one post-translational modification modifies another. This Comment highlights its discovery, mechanistic basis and functional consequences, and outlines critical questions for understanding this emerging signaling paradigm.

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