KEGG for taxonomy-based analysis of pathways and genomes

KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database entry) is identified by the KEGG identifier (kid), which generally takes the form of a prefix followed b...

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Published in:	Nucleic acids research Vol. 51; no. D1; pp. D587 - D592
Main Authors:	Kanehisa, Minoru, Furumichi, Miho, Sato, Yoko, Kawashima, Masayuki, Ishiguro-Watanabe, Mari
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 06.01.2023
Subjects:	Database Issue Databases, Factual Databases, Genetic Genome Genomics - methods
ISSN:	0305-1048, 1362-4962, 1362-4962
Online Access:	Get full text
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Abstract	KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database entry) is identified by the KEGG identifier (kid), which generally takes the form of a prefix followed by a five-digit number, and can be retrieved by appending /entry/kid in the URL. The KEGG pathway map viewer, the Brite hierarchy viewer and the newly released KEGG genome browser can be launched by appending /pathway/kid, /brite/kid and /genome/kid, respectively, in the URL. Together with an improved annotation procedure for KO (KEGG Orthology) assignment, an increasing number of eukaryotic genomes have been included in KEGG for better representation of organisms in the taxonomic tree. Multiple taxonomy files are generated for classification of KEGG organisms and viruses, and the Brite hierarchy viewer is used for taxonomy mapping, a variant of Brite mapping in the new KEGG Mapper suite. The taxonomy mapping enables analysis of, for example, how functional links of genes in the pathway and physical links of genes on the chromosome are conserved among organism groups.
AbstractList	KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database entry) is identified by the KEGG identifier (kid), which generally takes the form of a prefix followed by a five-digit number, and can be retrieved by appending /entry/kid in the URL. The KEGG pathway map viewer, the Brite hierarchy viewer and the newly released KEGG genome browser can be launched by appending /pathway/kid, /brite/kid and /genome/kid, respectively, in the URL. Together with an improved annotation procedure for KO (KEGG Orthology) assignment, an increasing number of eukaryotic genomes have been included in KEGG for better representation of organisms in the taxonomic tree. Multiple taxonomy files are generated for classification of KEGG organisms and viruses, and the Brite hierarchy viewer is used for taxonomy mapping, a variant of Brite mapping in the new KEGG Mapper suite. The taxonomy mapping enables analysis of, for example, how functional links of genes in the pathway and physical links of genes on the chromosome are conserved among organism groups. KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database entry) is identified by the KEGG identifier (kid), which generally takes the form of a prefix followed by a five-digit number, and can be retrieved by appending /entry/kid in the URL. The KEGG pathway map viewer, the Brite hierarchy viewer and the newly released KEGG genome browser can be launched by appending /pathway/kid, /brite/kid and /genome/kid, respectively, in the URL. Together with an improved annotation procedure for KO (KEGG Orthology) assignment, an increasing number of eukaryotic genomes have been included in KEGG for better representation of organisms in the taxonomic tree. Multiple taxonomy files are generated for classification of KEGG organisms and viruses, and the Brite hierarchy viewer is used for taxonomy mapping, a variant of Brite mapping in the new KEGG Mapper suite. The taxonomy mapping enables analysis of, for example, how functional links of genes in the pathway and physical links of genes on the chromosome are conserved among organism groups.KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database entry) is identified by the KEGG identifier (kid), which generally takes the form of a prefix followed by a five-digit number, and can be retrieved by appending /entry/kid in the URL. The KEGG pathway map viewer, the Brite hierarchy viewer and the newly released KEGG genome browser can be launched by appending /pathway/kid, /brite/kid and /genome/kid, respectively, in the URL. Together with an improved annotation procedure for KO (KEGG Orthology) assignment, an increasing number of eukaryotic genomes have been included in KEGG for better representation of organisms in the taxonomic tree. Multiple taxonomy files are generated for classification of KEGG organisms and viruses, and the Brite hierarchy viewer is used for taxonomy mapping, a variant of Brite mapping in the new KEGG Mapper suite. The taxonomy mapping enables analysis of, for example, how functional links of genes in the pathway and physical links of genes on the chromosome are conserved among organism groups.
Author	Kawashima, Masayuki Ishiguro-Watanabe, Mari Sato, Yoko Furumichi, Miho Kanehisa, Minoru
Author_xml	– sequence: 1 givenname: Minoru orcidid: 0000-0001-6123-540X surname: Kanehisa fullname: Kanehisa, Minoru – sequence: 2 givenname: Miho surname: Furumichi fullname: Furumichi, Miho – sequence: 3 givenname: Yoko surname: Sato fullname: Sato, Yoko – sequence: 4 givenname: Masayuki surname: Kawashima fullname: Kawashima, Masayuki – sequence: 5 givenname: Mari surname: Ishiguro-Watanabe fullname: Ishiguro-Watanabe, Mari
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/36300620$$D View this record in MEDLINE/PubMed
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Cites_doi	10.1002/pro.4172 10.1093/nar/gkab1112 10.1093/nar/gkab1135 10.1093/nar/gkx932 10.1002/pro.3715 10.1093/nar/gkv1189 10.1093/nar/gkaa970 10.1093/nar/gkr1178 10.1126/science.7542800 10.1093/nar/gkv1226
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Copyright	The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. 2023
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References	Kanehisa (2023010804254585600_B1) 2021; 49 Kitts (2023010804254585600_B10) 2016; 44 Federhen (2023010804254585600_B8) 2012; 40 Sayers (2023010804254585600_B7) 2022; 50 O’Leary (2023010804254585600_B6) 2016; 44 Kanehisa (2023010804254585600_B3) 2019; 28 Kanehisa (2023010804254585600_B2) 2022; 31 Fleischmann (2023010804254585600_B4) 1995; 269 Sayers (2023010804254585600_B5) 2022; 50 Lefkowitz (2023010804254585600_B9) 2018; 46
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