Tessera

WikiPathways

@wikipathways.fosstodon.org.ap.brid.gy

WikiPathways is an open, public platform dedicated to the collection and curation of biological pathways by and for the scientific community 🌉 bridged from ⁂ https://fosstodon.org/@wikipathways, follow @ap.brid.gy to interact

54 Posts42 Follower 3 Folgt

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 4w ago

July 2026 WikiPathways update: 31 edits in 5 pathways by 4 contributorsin and 1 new pathway. More news at https://github.com/wikipathways/wikipathways-help/discussions/236 https://www.wikipathways.org/index.php/Download_Pathways #bioinformatics #openscience #opensource

2026 July Release and other news · wikipathways wikipathways-help · Discussion #236

The 2026 July Release is available for download. This release has 31 edit in 5 pathways by 4 authors, and 1 new pathways. Other news Press, articles, blog posts, videos Altantic cod is a new organi...

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WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · last mo.

you can now share pathways with a few clicks on Mastodon (thx to the PR by @larsgw) Click on the orange arrow bottom left of the pathway figure, click the Mastodon logo, and get a window to share on your fediverse server #fediverse #openscience #mastodon #biology

Screenshot of the https://www.wikipathways.org/pathways/WP5638 webpage, after clicking the orange "share" button (visible as the curve arrow mid left of the screenshot, right of the "download" icon). In front of it, it shows the WikiPathways "share" dialog with three URLs to share the page, but also a row of five logos for sharing to Facebook, Mastodon, Whatsapp, LinkedIn, and email (in that order). In front of all that, a second browser window with the Mastodon "Share to Mastodon" window, with the example text to share (defaulting to here to "Check out this pathway from @wikipathways@fosstodon.org: Fatty acid beta-oxidation https://www.wikipathways.org/instance/WP5638"), and a paragraph asking for "Your Mastodon Domain", and a big "Continue to Mastodon" button.

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · last mo.

Google Scholar now found >500 citations to the WikiPathways 2024 paper: https://scholar.google.com/scholar?oi=bibs&hl=en&cites=9841341872570789753 There are some interesting titles in that list of articles!

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 2mo ago

June 2026 WikiPathways release: 10 edits by 5 contributors, with 2 new pathways. More news at https://github.com/wikipathways/wikipathways-help/discussions/233 #openscience

2026 June Release and other news · wikipathways wikipathways-help · Discussion #233

The 2026 June Release is available for download. Still not back at our regular activity, this release has 10 edit by 5 authors, and two new pathways. Other news Press, articles, blog posts, videos ...

github.com

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 2mo ago

a new R package, PinPath, allows mapping experimental data onto pathways, using just R: https://doi.org/doi:10.18129/B9.bioc.PinPath https://bioconductor.org/packages/devel/bioc/html/PinPath.html #openscience #bioinformatics #bioconductor

Example SVG from the WikiPathways vignette of the PinPath packages with data mapped onto a pathway. The pathways is from a publication from 2022: https://doi.org/10.3389/fonc.2022.849640 "A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma"

Genes/Proteins are colored by up- or downregulation, blue and red.

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 3mo ago

today we phased out the WikiPathways Classic website. This website has served the project for many years and was based on the @mediawiki software for the account administration features, extended with feature to display and edit pathways. Following upstream releases turned out costly and several […]

Original post on fosstodon.org

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WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 4mo ago

April 2026 WikiPathways update: 71 edits by 7 contributorsin and 2 new pathways the last month. More news at https://github.com/wikipathways/wikipathways-help/discussions/231 Accessible via #webservices, #rstats, #pathvisio and #cytoscape. https://www.wikipathways.org/index.php/Download_Pathways […]

Original post on fosstodon.org

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WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 4mo ago

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

Screenshot of part of the linked webpage. It shows a list ("Pathways Cited in the Literature"), stating the fact listed in the main post, and then an alphabetically sorted list of pathways by name (but also with WP identifier), and for each, as sublist, DOI / PubMedCentral ID badges for the articles that cite that pathway. The screenshot shows that the first 10 pathways in the list of 1, 2, or 3 citations.

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 4mo ago

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

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 4mo ago

@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

Screenshot of the linked SPARQL endpoint interface. It shows three main panels below a title bar (which includes the endpoint URL). One panel shows the title, description, and SPARQL query currently being "edited". The right-hand side panel shows a list of queries, now with easier to read query names. The bottom panel is still the results table. The query used is the one listing all authors, sorted descending by the number of pathways they initiated. For each author, the number of pathways, their name, ORCID, and WikiPathways account page is listed.

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 4mo ago

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

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 5mo ago

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 […]

Original post on fosstodon.org

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WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 5mo ago

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 […]

Original post on fosstodon.org

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WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 5mo ago

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/ […]

Original post on fosstodon.org

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WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 5mo ago

Original post on fosstodon.org

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 5mo ago

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]

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 6mo ago

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 […]

Original post on fosstodon.org

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WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 6mo ago

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 […]

Original post on fosstodon.org

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 7mo ago

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 […]

Original post on social.edu.nl

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WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 7mo ago

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 […]

Original post on fosstodon.org

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 7mo ago

"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 @wikipathways.fosstodon.org.ap.brid.gy · 8mo ago

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

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.

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 8mo ago

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

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.

Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 8mo ago

@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]

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

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 8mo ago

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" […]

Original post on fosstodon.org

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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 8mo ago

@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]

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.

LIPID MAPS @lipidmaps.bsky.social · 9mo ago

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

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 9mo ago

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/

Cloudflare Status

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

cloudflarestatus.com

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 9mo ago

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.

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 9mo ago