{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,25]],"date-time":"2026-10-25T12:35:32Z","timestamp":1792931732563,"version":"4.5.0"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2023,11,6]],"date-time":"2023-11-06T00:00:00Z","timestamp":1699228800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM103504"],"award-info":[{"award-number":["GM103504"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM100039"],"award-info":[{"award-number":["GM100039"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001826","name":"ZonMw","doi-asserted-by":"publisher","award":["10430012010015"],"award-info":[{"award-number":["10430012010015"]}],"id":[{"id":"10.13039\/501100001826","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003246","name":"NWO","doi-asserted-by":"publisher","award":["VHP4Safety NWA-ORC 1292.19.272"],"award-info":[{"award-number":["VHP4Safety NWA-ORC 1292.19.272"]}],"id":[{"id":"10.13039\/501100003246","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union\u2019s Horizon 2020","award":["863059"],"award-info":[{"award-number":["863059"]}]},{"name":"European Union\u2019s Horizon 2020","award":["814572"],"award-info":[{"award-number":["814572"]}]},{"name":"European Union\u2019s Horizon 2020","award":["814425"],"award-info":[{"award-number":["814425"]}]},{"name":"European Union\u2019s Horizon 2020","award":["825575"],"award-info":[{"award-number":["825575"]}]},{"name":"ELIXIR Europe"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>WikiPathways (wikipathways.org) is an open-source biological pathway database. Collaboration and open science are pivotal to the success of WikiPathways. Here we highlight the continuing efforts supporting WikiPathways, content growth\u00a0and collaboration among pathway researchers. As an evolving database, there is a growing need for WikiPathways to address and overcome technical challenges. In this direction, WikiPathways has undergone major restructuring, enabling a renewed approach for sharing and curating pathway knowledge, thus providing stability for the future of community pathway curation. The website has been redesigned to improve and enhance user experience. This next generation of WikiPathways continues to support existing features while improving maintainability of the database and facilitating community input by providing new functionality and leveraging automation.<\/jats:p>","DOI":"10.1093\/nar\/gkad960","type":"journal-article","created":{"date-parts":[[2023,10,13]],"date-time":"2023-10-13T16:09:38Z","timestamp":1697213378000},"page":"D679-D689","source":"Crossref","is-referenced-by-count":542,"title":["WikiPathways 2024: next generation pathway database"],"prefix":"10.1093","volume":"52","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2940-8926","authenticated-orcid":false,"given":"Ayushi","family":"Agrawal","sequence":"first","affiliation":[{"name":"Data Science and Biotechnology, Gladstone Institutes , San Francisco, CA, 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8319-7758","authenticated-orcid":false,"given":"Hasan","family":"Balc\u0131","sequence":"additional","affiliation":[{"name":"Maastricht Centre for Systems Biology (MaCSBio), Maastricht University , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5410-599X","authenticated-orcid":false,"given":"Kristina","family":"Hanspers","sequence":"additional","affiliation":[{"name":"Data Science and Biotechnology, Gladstone Institutes , San Francisco, CA, 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1224-9690","authenticated-orcid":false,"given":"Susan L","family":"Coort","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2230-0840","authenticated-orcid":false,"given":"Marvin","family":"Martens","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8449-1318","authenticated-orcid":false,"given":"Denise N","family":"Slenter","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7770-620X","authenticated-orcid":false,"given":"Friederike","family":"Ehrhart","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5934-3559","authenticated-orcid":false,"given":"Daniela","family":"Digles","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, University of Vienna , Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9773-4008","authenticated-orcid":false,"given":"Andra","family":"Waagmeester","sequence":"additional","affiliation":[{"name":"Micelio BV , Ekeren, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-2045-4009","authenticated-orcid":false,"given":"Isabel","family":"Wassink","sequence":"additional","affiliation":[{"name":"Maastricht Centre for Systems Biology (MaCSBio), Maastricht University , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4904-3269","authenticated-orcid":false,"given":"Tooba","family":"Abbassi-Daloii","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1661-6304","authenticated-orcid":false,"given":"Elisson N","family":"Lopes","sequence":"additional","affiliation":[{"name":"Department of Epigenetics. Van Andel Institute , Grand Rapids, MI\u00a049503, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2878-4049","authenticated-orcid":false,"given":"Aishwarya","family":"Iyer","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4166-7093","authenticated-orcid":false,"given":"Javier\u00a0Mill\u00e1n","family":"Acosta","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4751-4637","authenticated-orcid":false,"given":"Lars G","family":"Willighagen","sequence":"additional","affiliation":[{"name":"Unaffiliated , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8501-7319","authenticated-orcid":false,"given":"Kozo","family":"Nishida","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4693-0591","authenticated-orcid":false,"given":"Anders","family":"Riutta","sequence":"additional","affiliation":[{"name":"Data Science and Biotechnology, Gladstone Institutes , San Francisco, CA, 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helena","family":"Basaric","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5301-3142","authenticated-orcid":false,"given":"Chris\u00a0T","family":"Evelo","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7542-0286","authenticated-orcid":false,"given":"Egon L","family":"Willighagen","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7699-8191","authenticated-orcid":false,"given":"Martina","family":"Kutmon","sequence":"additional","affiliation":[{"name":"Maastricht Centre for Systems Biology (MaCSBio), Maastricht University , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5706-2163","authenticated-orcid":false,"given":"Alexander\u00a0R","family":"Pico","sequence":"additional","affiliation":[{"name":"Data Science and Biotechnology, Gladstone Institutes , San Francisco, CA, 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,11,6]]},"reference":[{"key":"2024010511444609800_B1","doi-asserted-by":"crossref","first-page":"D613","DOI":"10.1093\/nar\/gkaa1024","article-title":"WikiPathways: connecting communities","volume":"49","author":"Martens","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2024010511444609800_B2","doi-asserted-by":"crossref","first-page":"e184","DOI":"10.1371\/journal.pbio.0060184","article-title":"WikiPathways: pathway editing for the people","volume":"6","author":"Pico","year":"2008","journal-title":"PLoS Biol."},{"key":"2024010511444609800_B3","doi-asserted-by":"crossref","first-page":"963357","DOI":"10.3389\/fimmu.2022.963357","article-title":"Tissue-specific pathway activities: a retrospective analysis in COVID-19 patients","volume":"13","author":"Pham","year":"2022","journal-title":"Front. Immunol."},{"key":"2024010511444609800_B4","doi-asserted-by":"crossref","first-page":"btad118","DOI":"10.1093\/bioinformatics\/btad118","article-title":"NDEx IQuery: a multi-method network gene set analysis leveraging the network data exchange","volume":"39","author":"Pillich","year":"2023","journal-title":"Bioinformatics"},{"key":"2024010511444609800_B5","first-page":"100141","article-title":"clusterProfiler 4.0: a universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation (Camb)"},{"key":"2024010511444609800_B6","doi-asserted-by":"crossref","first-page":"btac726","DOI":"10.1093\/bioinformatics\/btac726","article-title":"RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes","volume":"39","author":"Braisted","year":"2023","journal-title":"Bioinformatics"},{"key":"2024010511444609800_B7","doi-asserted-by":"crossref","first-page":"1.30.1","DOI":"10.1002\/cpbi.5","article-title":"The GeneCards suite: from gene data mining to disease genome sequence analyses","volume":"54","author":"Stelzer","year":"2016","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"2024010511444609800_B8","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1186\/s13059-020-02181-2","article-title":"Pathway information extracted from 25 years of pathway figures","volume":"21","author":"Hanspers","year":"2020","journal-title":"Genome Biol."},{"key":"2024010511444609800_B9","doi-asserted-by":"crossref","first-page":"D1301","DOI":"10.1093\/nar\/gkr1074","article-title":"WikiPathways: building research communities on biological pathways","volume":"40","author":"Kelder","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2024010511444609800_B10","doi-asserted-by":"crossref","first-page":"e1004085","DOI":"10.1371\/journal.pcbi.1004085","article-title":"PathVisio 3: an extendable pathway analysis toolbox","volume":"11","author":"Kutmon","year":"2015","journal-title":"PLoS Comput. Biol."},{"key":"2024010511444609800_B11","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1007\/978-3-319-70407-4_36","article-title":"Scholia, Scientometrics and Wikidata","volume-title":"The Semantic Web: ESWC 2017 Satellite Events","author":"Nielsen","year":"2017"},{"key":"2024010511444609800_B12","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1007\/978-1-4939-6783-4_13","article-title":"NDEx: a community resource for sharing and publishing of biological networks","volume":"1558","author":"Pillich","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"2024010511444609800_B13","article-title":"Drugst.One \u2013 A plug-and-play solution for online systems medicine and network-based drug repurposing","author":"Maier","year":"2023"},{"key":"2024010511444609800_B14","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2024010511444609800_B15","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1471-2105-11-5","article-title":"The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services","volume":"11","author":"van\u00a0Iersel","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2024010511444609800_B16","first-page":"3275","article-title":"Cellular signaling pathways regulating \u03b2-cell proliferation as a promising therapeutic target in the treatment of diabetes","volume":"16","author":"Jiang","year":"2018","journal-title":"Exp. Ther. Med."},{"key":"2024010511444609800_B17","article-title":"JAK-STAT signaling in the regulation of Beta-cells (WP5358)","volume-title":"WikiPathways","author":"Wassink","year":"2023"},{"key":"2024010511444609800_B18","doi-asserted-by":"crossref","first-page":"e10851","DOI":"10.15252\/msb.202110851","article-title":"COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms","volume":"17","author":"Ostaszewski","year":"2021","journal-title":"Mol. Syst. Biol."},{"key":"2024010511444609800_B19","doi-asserted-by":"crossref","DOI":"10.1101\/2023.03.02.530766","article-title":"Molecular adverse outcome pathways: towards the implementation of transcriptomics data in risk assessments","author":"Martens","year":"2023"},{"key":"2024010511444609800_B20","doi-asserted-by":"crossref","first-page":"849640","DOI":"10.3389\/fonc.2022.849640","article-title":"A community-driven, openly accessible molecular pathway integrating knowledge on malignant pleural mesothelioma","volume":"12","author":"Martens","year":"2022","journal-title":"Front. Oncol."},{"key":"2024010511444609800_B21","doi-asserted-by":"crossref","first-page":"W90","DOI":"10.1093\/nar\/gkw377","article-title":"Enrichr: a comprehensive gene set enrichment analysis web server 2016 update","volume":"44","author":"Kuleshov","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2024010511444609800_B22","doi-asserted-by":"crossref","first-page":"2952","DOI":"10.1093\/bioinformatics\/btac172","article-title":"rbioapi: user-friendly R interface to biologic web services\u2019 API","volume":"38","author":"Rezwani","year":"2022","journal-title":"Bioinformatics"},{"key":"2024010511444609800_B23","doi-asserted-by":"crossref","first-page":"btac757","DOI":"10.1093\/bioinformatics\/btac757","article-title":"GSEApy: a comprehensive package for performing gene set enrichment analysis in Python","volume":"39","author":"Fang","year":"2023","journal-title":"Bioinformatics"},{"key":"2024010511444609800_B24","doi-asserted-by":"crossref","first-page":"152","DOI":"10.12688\/f1000research.4254.2","article-title":"WikiPathways app for cytoscape: making biological pathways amenable to network analysis and visualization","volume":"3","author":"Kutmon","year":"2014","journal-title":"F1000Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/52\/D1\/D679\/55040703\/gkad960.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/52\/D1\/D679\/55040703\/gkad960.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,5]],"date-time":"2024-01-05T07:15:18Z","timestamp":1704438918000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/52\/D1\/D679\/7369835"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11,6]]},"references-count":24,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2023,11,6]]},"published-print":{"date-parts":[[2024,1,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkad960","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,1,5]]},"published":{"date-parts":[[2023,11,6]]}}}