{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,11]],"date-time":"2026-05-11T14:15:38Z","timestamp":1778508938173,"version":"3.51.4"},"reference-count":10,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,11,6]],"date-time":"2019-11-06T00:00:00Z","timestamp":1572998400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U41HG003751"],"award-info":[{"award-number":["U41HG003751"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54GM114833"],"award-info":[{"award-number":["U54GM114833"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012116","name":"European Bioinformatics Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012116","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The Reactome Knowledgebase (https:\/\/reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism\u00a0and other cellular processes as an ordered network of molecular transformations in a single consistent data model, an extended version of a classic metabolic map. Reactome functions both as an archive of biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. To extend our ability to annotate human disease processes, we have implemented a new drug class and have used it initially to annotate drugs relevant to cardiovascular disease. Our annotation model depends on external domain experts to identify new areas for annotation and to review new content. New web pages facilitate recruitment of community experts and allow those who have contributed to Reactome to identify their contributions and link them to their ORCID records. To improve visualization of our content, we have implemented a new tool to automatically lay out the components of individual reactions with multiple options for downloading the reaction diagrams and associated data, and a new display of our event hierarchy that will facilitate visual interpretation of pathway analysis results.<\/jats:p>","DOI":"10.1093\/nar\/gkz1031","type":"journal-article","created":{"date-parts":[[2019,10,21]],"date-time":"2019-10-21T19:20:39Z","timestamp":1571685639000},"source":"Crossref","is-referenced-by-count":1095,"title":["The reactome pathway knowledgebase"],"prefix":"10.1093","author":[{"given":"Bijay","family":"Jassal","sequence":"first","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada"}]},{"given":"Lisa","family":"Matthews","sequence":"additional","affiliation":[{"name":"NYU School of Medicine, New York, NY 10016, USA"}]},{"given":"Guilherme","family":"Viteri","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK"}]},{"given":"Chuqiao","family":"Gong","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK"}]},{"given":"Pascual","family":"Lorente","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3288-8599","authenticated-orcid":false,"given":"Antonio","family":"Fabregat","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK"},{"name":"Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK"}]},{"given":"Konstantinos","family":"Sidiropoulos","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK"}]},{"given":"Justin","family":"Cook","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada"}]},{"given":"Marc","family":"Gillespie","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada"},{"name":"College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA"}]},{"given":"Robin","family":"Haw","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada"}]},{"given":"Fred","family":"Loney","sequence":"additional","affiliation":[{"name":"Oregon Health and Science University, Portland, OR 97239, USA"}]},{"given":"Bruce","family":"May","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada"}]},{"given":"Marija","family":"Milacic","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada"}]},{"given":"Karen","family":"Rothfels","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada"}]},{"given":"Cristoffer","family":"Sevilla","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK"}]},{"given":"Veronica","family":"Shamovsky","sequence":"additional","affiliation":[{"name":"NYU School of Medicine, New York, NY 10016, USA"}]},{"given":"Solomon","family":"Shorser","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada"}]},{"given":"Thawfeek","family":"Varusai","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK"}]},{"given":"Joel","family":"Weiser","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada"}]},{"given":"Guanming","family":"Wu","sequence":"additional","affiliation":[{"name":"Oregon Health and Science University, Portland, OR 97239, USA"}]},{"given":"Lincoln","family":"Stein","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada"},{"name":"Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8479-0262","authenticated-orcid":false,"given":"Henning","family":"Hermjakob","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK"},{"name":"National Center for Protein Sciences, Beijing, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5494-626X","authenticated-orcid":false,"given":"Peter","family":"D\u2019Eustachio","sequence":"additional","affiliation":[{"name":"NYU School of Medicine, New York, NY 10016, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,11,6]]},"reference":[{"key":"2019110606360308300_B1","doi-asserted-by":"crossref","first-page":"D596","DOI":"10.1093\/nar\/gky876","article-title":"Updates in Rhea: SPARQLing biochemical reaction data","volume":"47","author":"Lombardot","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019110606360308300_B2","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gky962","article-title":"New approach for understanding genome variations in KEGG","volume":"47","author":"Kanehisa","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019110606360308300_B3","doi-asserted-by":"crossref","first-page":"D633","DOI":"10.1093\/nar\/gkx935","article-title":"The MetaCyc database of metabolic pathways and enzymes","volume":"46","author":"Caspi","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019110606360308300_B4","doi-asserted-by":"crossref","first-page":"D419","DOI":"10.1093\/nar\/gky1038","article-title":"PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools","volume":"47","author":"Mi","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019110606360308300_B5","doi-asserted-by":"crossref","first-page":"D649","DOI":"10.1093\/nar\/gkx1132","article-title":"The reactome pathway knowledgebase","volume":"46","author":"Fabregat","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2019110606360308300_B6","doi-asserted-by":"crossref","first-page":"D481","DOI":"10.1093\/nar\/gkv1351","article-title":"The reactome pathway knowledgebase","volume":"44","author":"Fabregat","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019110606360308300_B7","doi-asserted-by":"crossref","first-page":"D1071","DOI":"10.1093\/nar\/gku1011","article-title":"Disease ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data","volume":"43","author":"Kibbe","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2019110606360308300_B8","doi-asserted-by":"crossref","first-page":"D1091","DOI":"10.1093\/nar\/gkx1121","article-title":"The IUPHAR\/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY","volume":"46","author":"Harding","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019110606360308300_B9","doi-asserted-by":"crossref","first-page":"D1214","DOI":"10.1093\/nar\/gkv1031","article-title":"ChEBI in 2016: Improved services and an expanding collection of metabolites","volume":"44","author":"Hastings","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2019110606360308300_B10","doi-asserted-by":"crossref","first-page":"D330","DOI":"10.1093\/nar\/gky1055","article-title":"The gene ontology resource: 20 years and still GOing strong","volume":"47","author":"GO Consortium","year":"2019","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/advance-article-pdf\/doi\/10.1093\/nar\/gkz1031\/30437527\/gkz1031.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/advance-article-pdf\/doi\/10.1093\/nar\/gkz1031\/30437527\/gkz1031.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,11,6]],"date-time":"2019-11-06T11:36:12Z","timestamp":1573040172000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/advance-article\/doi\/10.1093\/nar\/gkz1031\/5613674"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,11,6]]},"references-count":10,"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz1031","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,11,6]]},"article-number":"gkz1031"}}