WikiPathways
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wikipathways.fosstodon.org.ap.brid.gy
WikiPathways
@wikipathways.fosstodon.org.ap.brid.gy
32 followers 3 following 29 posts
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 on the fediverse by https://fed.brid.gy/ ]
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wikipathways.fosstodon.org.ap.brid.gy
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.
November 15, 2025 at 11:54 AM
wikipathways.fosstodon.org.ap.brid.gy
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
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 12, 2025 at 6:21 AM
wikipathways.fosstodon.org.ap.brid.gy
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]
Depiction of the caffeine synthesis pathway in Coffea arabica showing a 6-step biosynthesis starting with xanthosine monophosphate, involving 5 proteins.
October 18, 2025 at 11:10 AM
wikipathways.fosstodon.org.ap.brid.gy
August 2025 WikiPathways release: 367 edits by 10 contributors and 26 new pathways.

https://data.wikipathways.org/

#openscience #biology #pfas
WP5579 shows two lists of PFAS, one found in all sampled humans, the second list in 10-99% of the sampled humans. The description of the pathway writes: "A recent study by the Dutch RIVM found that across The Netherlands seven PFAS are found in every tested human, with an additional nine found in at least 10% of the population. Three of these PFAS were found to be associated to cancer. PFOS, PFHxS, and PFOA were found to be significantly positively associated with testicular germ cell tumors (TGCT) among U.S. Air Force servicemen [PMID:37458713 ]. Data from a 2-year bioassay study on rats did not support a PFOS-related effect on testicular tumors, while serum PFOS concentrations were much higher in magnitude compared to levels reported in the former study [PMID:37751326]. ..." A depiction of WP5633, with the description: "RNA Polymerase II transcription: the preinitiation complex."
August 10, 2025 at 6:57 PM
wikipathways.fosstodon.org.ap.brid.gy
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]
Screenshot of the linked PFOCR website's search results for APOE4, showing 4 (and a half) results, each one with a thumbnail of the pathway on the left, the title of the article, publication year, and a short description. Page of PFOCR where article titles are listed that have been digitized in WikiPathways, along with a badge at the end showing the matching WikiPathways WP identifier. For example, the top item reads: Regulation of D-secretase in neurodegenerative diseases (2020, Mus musculus,Rattus norvegicus,Homo sapiens,Sar) WikiPathways WP5372
August 5, 2025 at 8:13 PM
wikipathways.fosstodon.org.ap.brid.gy
our new website has a full overview at https://www.wikipathways.org/browse/citedin

You may not differences in the numbers. One reason is that not all cited pathways are in fact on the new website

#bioinformatics
Screenshot of the linked page, stating that "772 pathways have been cited a total of 2134 times". The latter is higher (more citations were added since the previous post), but the number of pathways is lower. The page shows a list, of which the first eight pathway names are visible, each with one or more PubMed Central IDs or DOIs, shown as a badge in grey ("PMC" or "DOI") and blue (the identifier).
July 27, 2025 at 1:33 PM
wikipathways.fosstodon.org.ap.brid.gy
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]
"Cited In" section for WP3947 showing a list with two articles, "Genetic risk of depression is different in subgroups of dietary ratio of tryptophan to large neutral amino acids (2023)" and "Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma (2022)". The list is followed by the text "Are you planning to include this pathway in your next publication? See How to Cite and add a link here to your paper once it's online."
July 27, 2025 at 8:51 AM
wikipathways.fosstodon.org.ap.brid.gy
July 2025 WikiPathways release: 531 edits by 15 contributors and 2 new pathways.

https://data.wikipathways.org/

#openscience #biology #RareDisease
Drawing of the pathway WP5580 with this description: "In decidual NK (dNK) cells, killer-cell immunoglobulin-like receptors (KIRs) interact with HLA-C allotypes on extravillous trophoblast (EVT) cells to modulate immune responses at the maternal–fetal interface. Inhibitory KIRs transmit signals through immunoreceptor tyrosine-based inhibitory motifs (ITIMs), which recruit SHP-1 and SHP-2 phosphatases to suppress activation pathways. Conversely, activating KIRs signal via the adaptor protein DAP12, whose ITAM motifs recruit SYK kinase, leading to downstream activation of LAT, SLP-76, VAV1, PLC-γ1, and NF-κB. This cascade promotes cytokine production and functional activation of dNK cells. Additionally, KIR signaling has been linked to repeated pregnancy loss (RPL), suggesting coordination between immune signaling and placental development mediated by dNK cells. The exact origin of dNK cells (phenotype CD56⁺⁺ (bright) CD16⁻) is still uncertain. Some studies suggest they may arise from CD34⁺ progenitor cells, while others propose that peripheral blood NK (pbNK) cells or local NK precursors give rise to uterine NK (uNK) cells. These uNK cells may then differentiate into either endometrial NK (eNK) cells, which are present before pregnancy, or decidual NK (dNK) cells, which appear during early pregnancy." Drawing of pathway WP5570 with the description: "This Pathway is a schematic representation of Glycerol metabolism, which is an important intermediate metabolite, acting as a bridge between carbohydrate and lipid metabolism. This pathway also depicts inherited metabolic diseases that disrupt glycerol metabolism including: Glycerol kinase deficiency, Glycerate kinase deficiency, Aquaporin 7 deficiency and Cytosolic glycerol-3-phosphate dehydrogenase deficiency. This pathway was inspired by chapter 49 (Disorders of Glycerol Metabolism) of the book of Blau (ISBN 978-3-030-67726-8)."
July 13, 2025 at 7:49 AM
wikipathways.fosstodon.org.ap.brid.gy
June 2025 WikiPathways release: 338 edits by 15 contributors and 9 new pathways. https://data.wikipathways.org/

Accessible via #webservices, #rstats, Pathvisio, and Cytoscape.
Depiction of the pathway "Lupus pathogenesis" (WP5559): "Systemic lupus erythematosus (SLE) is an autoimmune disease in which the body’s immune system mistakenly attacks its own tissues. It can lead to lupus nephritis, where the kidneys become inflamed. This causes impaired kidney function and, in severe cases, kidney failure. Lupus has an incidence of around 5 per 100,000 person-years, and affects women much more frequently than men. ..." Depiction of the pathway "Atopic dermatitis mechanism and therapies" (WP5538): "Atopic dermatitis (AD), also known as atopic eczema, arises from a complex interplay of genetic susceptibility and environmental triggers that disrupt the skin barrier. This dysfunction is exacerbated by alterations in the skin microbiome—particularly a reduction in Staphylococcus epidermidis and an overgrowth of Staphylococcus aureus—which increase the skin’s vulnerability to external allergens. Keratinocytes, in response to this disruption, release epithelial-derived cytokines such as thymic stromal lymphopoietin (TSLP), interleukin (IL)-25, and IL-33. These cytokines promote type 2 immune responses by activating group 2 innate lymphoid cells (ILC2s), T helper 2 (Th2) cells, and T follicular helper 2 (Tfh2) cells. ..." Depiction of the pathway "Lupus therapies" (WP5560): "Therapeutic approaches in systemic lupus erythematosus (SLE) increasingly focus on modulating B and T cell activity. B cell–directed therapies involve targeting specific surface receptors such as CD19, CD20, CD22, CD38, and CD40, as well as blocking B cell-related cytokines like BAFF (B-cell activating factor, also known as TNFSF13B). T cell-focused strategies include blocking co-stimulatory pathways (e.g. CD40–CD40L, CD80/86–CD28, ICOS–ICOSL) and inhibiting pro-inflammatory cytokines, including IL-6, IL-12, IL-17, IL-23, and IFN-γ. Inspired by Figure 1 in Su et al. (2024)."
June 11, 2025 at 7:04 PM
wikipathways.fosstodon.org.ap.brid.gy
May 2025 WikiPathways release: 491 edits by 9 contributors and 8 new pathways.

Accessible via #webservices, #rstats, Pathvisio, and Cytoscape.

#biology #bioinformatics
Image of the Visual cycle (WP5534) pathway. https://www.wikipathways.org/pathways/WP5534 Description: "The visual cycle, also known as the retinoid cycle metabolic pathway, regenerates vitamin A derived chromophore 11-cis retinal. This enables visual phototransduction response to light. Inspired by rgd.mcw.edu/rgdweb/pathway/pathwayRecord.html?acc_id=PW:0001005." Image of the Atopic dermatitis mechanism and therapies (WP5538) pathway. https://www.wikipathways.org/pathways/WP5538 Description: "Atopic dermatitis (AD), also known as atopic eczema, arises from a complex interplay of genetic susceptibility and environmental triggers that disrupt the skin barrier. This dysfunction is exacerbated by alterations in the skin microbiome—particularly a reduction in Staphylococcus epidermidis and an overgrowth of Staphylococcus aureus—which increase the skin’s vulnerability to external allergens. Keratinocytes, in response to this disruption, release epithelial-derived cytokines such as thymic stromal lymphopoietin (TSLP), interleukin (IL)-25, and IL-33. These cytokines promote type 2 immune responses by activating group 2 innate lymphoid cells (ILC2s), T helper 2 (Th2) cells, and T follicular helper 2 (Tfh2) cells. These lymphocytes, stimulated by activated Langerhans cells (LCs) and inflammatory dendritic epidermal cells (IDECs), subsequently secrete IL-4, IL-5, and IL-13. IL-4 and IL-13 signal through type I (IL-4Rα / CD132) and type II (IL-4Rα / IL-13Rα1) receptors expressed on B cells, keratinocytes, and sensory neurons, activating the JAK-STAT signaling pathway. Tfh2 cells promote class switching to IgE in B cells, enhancing mast cell and basophil activation via FcεRI. [..]" Image of the Fibrotic response of human trabecular meshwork cells to transforming growth factor-beta 3 (TGFB3 and autotaxin (ENPP2, or ATX) in aqueous humor (WP5545) pathway. https://www.wikipathways.org/pathways/WP5545 Description: "This pathway visualises the potential mechanisms of TGF-β3-mediated ENPP2 (or ATX) expression and fibrotic changes in HTM cells. This pathway was created based on the PFOCR project, https://pfocr.wikipathways.org/figures/PMC9496180__biomolecules-12-01231-g008.html" Image of the Multiple sclerosis mechanism and therapies (WP5540) pathway. https://www.wikipathways.org/pathways/WP5540 Description: "This diagram shows the immunopathogenesis of multiple sclerosis (MS) and therapeutic targets. Available therapies for MS act through a range of mechanisms, including pleiotropic effects, immune cell depletion, inhibition of proliferation, and blockade of cell migration. These intervene at various stages of the inflammatory process. Treatments exert their effects across the peripheral immune system, the blood–brain barrier, and within the central nervous system (CNS) itself. Inspired by Figure 1 in Bierhansl et al. (2022)."
May 11, 2025 at 10:09 AM
wikipathways.fosstodon.org.ap.brid.gy
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]
Screenshot of the Day 1 page, showing a network of bio things, from symptoms, via disease, gene, protein, to medication, with some side branched. Below this, the program of Day 1, with various lectures on (success stories using) disease mapping approaches. Below that, the faces of the six organizers from the ERDERA project, including Friederike Ehrhart, Eleni Mina, Anais Baudot, Alexandra Valeanu, Galadriel Briere, and Daphne Wijnbergen.
April 20, 2025 at 6:01 PM
wikipathways.fosstodon.org.ap.brid.gy
: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
new pathway: "Age-related macular degeneration (WP5526)" "Age-related macular degeneration (AMD) is a leading cause of vision impairment in individuals aged 55 and older in the Western world. This diagram shows metabolic pathway crosstalk in AMD. In AMD, the upregulation of PARP2 expression leads to the downregulation of SIRT1. The depletion of SIRT1, a NAD+-dependent deacetylase, causes acetylation and inactivation of PGC-1α." new pathway: "Retinoid metabolism in retina: healthy vs. RLBP1-deficient (WP5532)" "RLBP1 encodes CRALBP, a cellular retinaldehyde-binding protein that functions as a soluble retinoid carrier in the visual cycle of the eye. Mutations in RLBP1 are linked to recessively inherited conditions, such as Bothnia dystrophy, retinitis pigmentosa, retinitis punctata albescens, fundus albipunctatus, and Newfoundland rod-cone dystrophy." new pathway: "Aspirin prevention of cancer metastasis (WP5518)" "Platelets generate TXA2, which binds to its receptor (TP) on T cells, initiating the activation of ARHGEF1, a guanine exchange factor that promotes the conversion of RhoA from its inactive GDP-bound state to its active GTP-bound form. This RhoA activation inhibits TCR-induced kinase pathways, T cell proliferation, and effector functions, ultimately suppressing anti-metastatic immunity. TXA2 production by platelets is COX1-dependent and can be blocked by aspirin or COX-1 selective inhibitors, which relieve T cells from TXA2-mediated suppression. Inspired by figure 14 in in Yang et al. (2025)."
April 10, 2025 at 6:26 PM
wikipathways.fosstodon.org.ap.brid.gy
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
Human pathway for "IL23 inhibitors in inflammatory bowel disease" (WP5516): "IL23 inhibitor drugs decrease an intestinal immune response that contributes to inflammatory bowel disease (IBD), like Crohn’s disease and ulcerative colitis. IL23 inhibitors like risankizumab (Skyrizi), guselkumab (Tremfya), mirikizumab (Omvoh), and brazikumab (MEDI2070) bind to IL23p19 (a.k.a. p19), the protein product of gene IL23A. That in turn blocks IL23A protein from binding to its receptor in immune cells, preventing the production of downstream inflammatory interleukins, cytokines, and other factors that manifest as IBD. IL-23 plays a crucial role in immune responses, especially in the intestinal mucosa. It has a novel p19 protein subunit, which interacts with the p40 subunit. This interaction activates the STAT4-JAK2 pathway. "
March 10, 2025 at 9:00 PM
wikipathways.fosstodon.org.ap.brid.gy
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
New pathway "Mitochondrial carrier deficiency associated with shuttle disturbances (WP5507)" https://www.wikipathways.org/pathways/WP5507 "Reflecting the pathway as shown in Figure 43.2 of Blau et al. "Physician’s guide to the diagnosis, treatment, and follow-up of inherited metabolic diseases" New pathway "GIP and GLP-1 function by tissue (WP5509)" https://www.wikipathways.org/pathways/WP5509 "Functions of GIP and GLP-1, two agonists of which are found in the weight-loss drug tirzepatide (a.k.a. Mounjaro). "Pancreatic and exopancreatic function of glucose‐dependent insulinotropic polypepide (GIP) and glucagon‐like peptide (GLP)‐1. GIP acts directly on the endocrine pancreas, bone, fat, gastrointestinal (GI) tract and brain. GLP‐1 acts directly on the endocrine pancreas, gastrointestinal tract, heart and brain." From Figure 2 in https://pmc.ncbi.nlm.nih.gov/articles/PMC4020673/." New pathway: "Vedolizumab therapy for irritable bowel syndrome (WP5512)" https://www.wikipathways.org/pathways/WP5512 "Vedolizumab is a humanized monoclonal antibody with a predominantly gastrointestinal effect. It specifically inhibits leucocyte integrin α4β7, thus preventing its interaction with mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1), which is involved in the migration of lymphocytes from the blood stream to the intestinal tissue. Vedolizumab is indicated in the treatment of moderate to severe active Crohn's disease and ulcerative colitis in adult patients with poor response, loss of response, or intolerance to conventional treatment or to tumour necrosis factor alpha (TNF-α) antagonists." Inspired by Figure 1 in https://pubmed.ncbi.nlm.nih.gov/31470005/. Vedolizumab is also known by its trade name, Entyvio. New pathway: "NSAIDs mechanism of action (WP5513)" https://www.wikipathways.org/pathways/WP5513 "Nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit the cyclooxygenase isoenzymes COX1 and COX2 with varying degrees of specificity for the COX2 isoform. As a result, the conversion of arachidonic acid to prostaglandins (PGs) is inhibited. The main effects of PGs throughout the body are listed." Inspired by Figure 1 in PMID:32322101.
February 11, 2025 at 6:38 AM
wikipathways.fosstodon.org.ap.brid.gy
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
Screenshot of the WikiPathways SPARQL user interface, showing the SPARQL query to list a table (with the first few rows at the bottom) listing diseases and the number of pathways annotated with them. On the right we see a folder structure with other examples queries.
November 25, 2024 at 5:12 PM