{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T02:54:34Z","timestamp":1793242474850,"version":"4.5.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2024,10,17]],"date-time":"2024-10-17T00:00:00Z","timestamp":1729123200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"NBDC Database Integration Coordination Program","award":["JPMJND2203"],"award-info":[{"award-number":["JPMJND2203"]}]},{"DOI":"10.13039\/501100002241","name":"Japan Science and Technology Agency","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002241","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>KEGG (https:\/\/www.kegg.jp\/) is a database resource for representation and analysis of biological systems. Pathway maps are the primary dataset in KEGG representing systemic functions of the cell and the organism in terms of molecular interaction and reaction networks. The KEGG Orthology (KO) system is a mechanism for linking genes and proteins to pathway maps and other molecular networks. Each KO is a generic gene identifier and each pathway map is created as a network of KO nodes. This architecture enables KEGG pathway mapping to uncover systemic features from KO assigned genomes and metagenomes. Additional roles of KOs include characterization of conserved genes and conserved units of genes in organism groups, which can be done by taxonomy mapping. A new tool has been developed for identifying conserved gene orders in chromosomes, in which gene orders are treated as sequences of KOs. Furthermore, a new dataset called VOG (virus ortholog group) is computationally generated from virus proteins and expanded to proteins of cellular organisms, allowing gene orders to be compared as VOG sequences as well. Together with these datasets and analysis tools, new types of pathway maps are being developed to present a global view of biological processes involving multiple organism groups.<\/jats:p>","DOI":"10.1093\/nar\/gkae909","type":"journal-article","created":{"date-parts":[[2024,10,2]],"date-time":"2024-10-02T07:18:46Z","timestamp":1727853526000},"page":"D672-D677","source":"Crossref","is-referenced-by-count":2989,"title":["KEGG: biological systems database as a model of the real world"],"prefix":"10.1093","volume":"53","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6123-540X","authenticated-orcid":false,"given":"Minoru","family":"Kanehisa","sequence":"first","affiliation":[{"name":"Institute for Chemical Research, Kyoto University , Uji , Kyoto 611-0011 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miho","family":"Furumichi","sequence":"additional","affiliation":[{"name":"Institute for Chemical Research, Kyoto University , Uji , Kyoto 611-0011 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoko","family":"Sato","sequence":"additional","affiliation":[{"name":"Pathway Solutions Inc. , 2-16-3 Higashi-Shinbashi, Minato-ku, Tokyo 105-0021 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuriko","family":"Matsuura","sequence":"additional","affiliation":[{"name":"Pathway Solutions Inc. , 2-16-3 Higashi-Shinbashi, Minato-ku, Tokyo 105-0021 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mari","family":"Ishiguro-Watanabe","sequence":"additional","affiliation":[{"name":"Human Genome Center, Institute of Medical Science, University of Tokyo , Minato-ku, Tokyo 108-8639 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,10,17]]},"reference":[{"key":"2025010610521641000_B1","doi-asserted-by":"crossref","first-page":"1947","DOI":"10.1002\/pro.3715","article-title":"Toward understanding the origin and evolution of cellular organisms","volume":"28","author":"Kanehisa","year":"2019","journal-title":"Protein Sci."},{"key":"2025010610521641000_B2","doi-asserted-by":"crossref","first-page":"D587","DOI":"10.1093\/nar\/gkac963","article-title":"KEGG for taxonomy-based analysis of pathways and genomes","volume":"51","author":"Kanehisa","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2025010610521641000_B3","doi-asserted-by":"crossref","first-page":"e4840","DOI":"10.1002\/pro.4820","article-title":"KEGG tools for classification and analysis of viral proteins","volume":"32","author":"Jin","year":"2023","journal-title":"Protein Sci."},{"key":"2025010610521641000_B4","first-page":"683","article-title":"DBGET\/LinkDB: an integrated database retrieval system","author":"Fujibuchi","year":"1998","journal-title":"Pac. 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I. A general method for finding local homologies and symmetries","volume":"10","author":"Goad","year":"1982","journal-title":"Nucleic Acids Res."},{"key":"2025010610521641000_B9","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","article-title":"Identification of common molecular subsequences","volume":"147","author":"Smith","year":"1981","journal-title":"J. Mol. Biol."},{"key":"2025010610521641000_B10","doi-asserted-by":"crossref","first-page":"baaa062","DOI":"10.1093\/database\/baaa062","article-title":"NCBI Taxonomy: a comprehensive update on curation, resources and tools","volume":"2020","author":"Schoch","year":"2020","journal-title":"Database"},{"key":"2025010610521641000_B11","doi-asserted-by":"crossref","first-page":"001840","DOI":"10.1099\/jgv.0.001840","article-title":"Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)","volume":"104","author":"Siddell","year":"2023","journal-title":"J. Gen. 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