{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T09:25:03Z","timestamp":1781861103602,"version":"3.54.5"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2019,10,5]],"date-time":"2019-10-05T00:00:00Z","timestamp":1570233600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM080746"],"award-info":[{"award-number":["GM080746"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>MetaCyc (MetaCyc.org) is a comprehensive reference database of metabolic pathways and enzymes from all domains of life. It contains 2749 pathways derived from more than 60\u00a0000 publications, making it the largest curated collection of metabolic pathways. The data in MetaCyc are evidence-based and richly curated, resulting in an encyclopedic reference tool for metabolism. MetaCyc is also used as a knowledge base for generating thousands of organism-specific Pathway\/Genome Databases (PGDBs), which are available in BioCyc.org and other genomic portals. This article provides an update on the developments in MetaCyc during September 2017 to August 2019, up to version 23.1. Some of the topics that received intensive curation during this period include cobamides biosynthesis, sterol metabolism, fatty acid biosynthesis, lipid metabolism, carotenoid metabolism, protein glycosylation, antibiotics and cytotoxins biosynthesis, siderophore biosynthesis, bioluminescence, vitamin K metabolism, brominated compound metabolism, plant secondary metabolism and human metabolism. Other additions include modifications to the GlycanBuilder software that enable displaying glycans using symbolic representation, improved graphics and fonts for web displays, improvements in the PathoLogic component of Pathway Tools, and the optional addition of regulatory information to pathway diagrams.<\/jats:p>","DOI":"10.1093\/nar\/gkz862","type":"journal-article","created":{"date-parts":[[2019,10,2]],"date-time":"2019-10-02T03:33:33Z","timestamp":1569987213000},"page":"D445-D453","source":"Crossref","is-referenced-by-count":1283,"title":["The MetaCyc database of metabolic pathways and enzymes - a 2019 update"],"prefix":"10.1093","volume":"48","author":[{"given":"Ron","family":"Caspi","sequence":"first","affiliation":[{"name":"SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Billington","sequence":"additional","affiliation":[{"name":"SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ingrid M","family":"Keseler","sequence":"additional","affiliation":[{"name":"SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anamika","family":"Kothari","sequence":"additional","affiliation":[{"name":"SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"Krummenacker","sequence":"additional","affiliation":[{"name":"SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6512-3296","authenticated-orcid":false,"given":"Peter E","family":"Midford","sequence":"additional","affiliation":[{"name":"SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wai Kit","family":"Ong","sequence":"additional","affiliation":[{"name":"SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5763-8935","authenticated-orcid":false,"given":"Suzanne","family":"Paley","sequence":"additional","affiliation":[{"name":"SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pallavi","family":"Subhraveti","sequence":"additional","affiliation":[{"name":"SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter D","family":"Karp","sequence":"additional","affiliation":[{"name":"SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,10,5]]},"reference":[{"key":"2020010521384541400_B1","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1093\/nar\/28.1.56","article-title":"The EcoCyc and MetaCyc databases","volume":"28","author":"Karp","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2020010521384541400_B2","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":"2020010521384541400_B3","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1093\/bib\/bbp043","article-title":"Pathway Tools version 13.0: integrated software for pathway\/genome informatics and systems biology","volume":"11","author":"Karp","year":"2010","journal-title":"Brief. Bioinform."},{"key":"2020010521384541400_B4","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1093\/bib\/bbv079","article-title":"Pathway Tools version 19.0 update: software for pathway\/genome informatics and systems biology","volume":"17","author":"Karp","year":"2016","journal-title":"Brief. Bioinform."},{"key":"2020010521384541400_B5","doi-asserted-by":"crossref","first-page":"424","DOI":"10.4056\/sigs.1794338","article-title":"The pathway tools pathway prediction algorithm","volume":"5","author":"Karp","year":"2011","journal-title":"Stand. Genomic Sci."},{"key":"2020010521384541400_B6","article-title":"The BioCyc collection of microbial genomes and metabolic pathways","author":"Karp","year":"2017","journal-title":"Brief. Bioinform."},{"key":"2020010521384541400_B7","doi-asserted-by":"crossref","first-page":"D517","DOI":"10.1093\/nar\/gkw1101","article-title":"MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes","volume":"45","author":"Vallenet","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020010521384541400_B8","doi-asserted-by":"crossref","first-page":"1806","DOI":"10.1104\/pp.109.136549","article-title":"A dynamic interface for capsaicinoid systems biology","volume":"150","author":"Mazourek","year":"2009","journal-title":"Plant Physiol."},{"key":"2020010521384541400_B9","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1104\/pp.16.01942","article-title":"Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants","volume":"173","author":"Schlapfer","year":"2017","journal-title":"Plant Physiol."},{"key":"2020010521384541400_B10","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1186\/s12918-016-0369-x","article-title":"The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize","volume":"10","author":"Walsh","year":"2016","journal-title":"BMC Syst. Biol."},{"key":"2020010521384541400_B11","doi-asserted-by":"crossref","first-page":"R84","DOI":"10.1186\/gb-2009-10-8-r84","article-title":"MouseCyc: a curated biochemical pathways database for the laboratory mouse","volume":"10","author":"Evsikov","year":"2009","journal-title":"Genome Biol."},{"key":"2020010521384541400_B12","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.1093\/glycob\/cwv091","article-title":"Symbol Nomenclature for Graphical Representations of Glycans","volume":"25","author":"Varki","year":"2015","journal-title":"Glycobiology"},{"key":"2020010521384541400_B13","doi-asserted-by":"crossref","first-page":"2162","DOI":"10.1016\/j.carres.2008.03.011","article-title":"GlycoCT-a unifying sequence format for carbohydrates","volume":"343","author":"Herget","year":"2008","journal-title":"Carbohydr. Res."},{"key":"2020010521384541400_B14","doi-asserted-by":"crossref","first-page":"1487","DOI":"10.1529\/biophysj.107.124784","article-title":"Group contribution method for thermodynamic analysis of complex metabolic networks","volume":"95","author":"Jankowski","year":"2008","journal-title":"Biophys. J."},{"key":"2020010521384541400_B15","doi-asserted-by":"crossref","DOI":"10.1002\/0471332607","volume-title":"Thermodynamics of Biochemical Reactions","author":"Alberty","year":"2003"},{"key":"2020010521384541400_B16","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1111\/febs.12530","article-title":"Fifty-five years of enzyme classification: advances and difficulties","volume":"281","author":"McDonald","year":"2014","journal-title":"FEBS J."},{"key":"2020010521384541400_B17","doi-asserted-by":"crossref","first-page":"4035","DOI":"10.1093\/nar\/gki711","article-title":"Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers","volume":"33","author":"Green","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2020010521384541400_B18","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1751-0473-2-3","article-title":"The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures","volume":"2","author":"Ceroni","year":"2007","journal-title":"Source Code Biol. Med."},{"key":"2020010521384541400_B19","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1515\/hsz-2012-0135","article-title":"The GlycanBuilder and GlycoWorkbench glycoinformatics tools: updates and new developments","volume":"393","author":"Damerell","year":"2012","journal-title":"Biol. Chem."},{"key":"2020010521384541400_B20","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":"2020010521384541400_B21","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1186\/1471-2105-14-112","article-title":"A systematic comparison of the MetaCyc and KEGG pathway databases","volume":"14","author":"Altman","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2020010521384541400_B22","doi-asserted-by":"crossref","DOI":"10.1128\/ecosalplus.ESP-0006-2018","article-title":"The EcoCyc Database","volume":"8","author":"Karp","year":"2018","journal-title":"EcoSal Plus"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D445\/31697668\/gkz862.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D445\/31697668\/gkz862.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,1,6]],"date-time":"2020-01-06T02:40:24Z","timestamp":1578278424000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/48\/D1\/D445\/5581728"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,10,5]]},"references-count":22,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2019,10,5]]},"published-print":{"date-parts":[[2020,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz862","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,1,8]]},"published":{"date-parts":[[2019,10,5]]}}}