KEGG Release Notes
See also GenomeNet release notes archive and past announcementsCurrent release
Release 112.1, December 1, 2024- For linking Japanese drug products to KEGG D numbers, a new code named YK code is made available (see Drug products in Japan and USA).
- The genome alignemnt tool accepts two types of comparisons: gene orders to be treated as KO sequences or VOG sequences.
- The PATHWAY database contains a new subcategory of overview maps presenting a global view of biological processes involving mutiple organism groupsm, such as Nitrogen cycle.
- This and other types of pathway maps contain direct links to Taxonomy mapping for a summary view of organism groups involved.
Past releases
Release 111.1, September 1, 2024- KEGG Syntax is reorganized as a collection of tools for taxonomy-based analysis of conserved genes (KOs and VOGs), conserved functional units of genes (modules) and conserved gene orders along the chromosomes of both cellular organisms and viruses.
- A new KEGG Mapper tool named MWsearch is made available allowing to use mass spectrometry data (molecular masses and chemical formulas) as query data, which are converted to KEGG IDs (C numbers).
- The "Change pathway type" button of KEGG pathway viewer now accepts multiple organism codes for combination or comparison of pathways. Global maps accept one additional code for 3-color display of two organisms, while regular maps accept more codes for split coloring display with the option of 3-color display for two organisms as well (see Color codes).
- Each of the reconstructed pathways in the KEGG Mapper Reconstruct tool may now be combined or compared with any KEGG organsim-specific pathway.
- The genome alignment tool is now associated with a graphical view of how segments of two genomes are related.
- A new resource named KEGG Syntax is released, together with a new tool for genome alignment, aiming to link positional correlations of genes to functional correlations.
- KEGG analysis tools, including KEGG Mapper, KEGG Web Apps and KEGG Syntax, are integrated in the same framework of web pages.
- The antialiasing for generating png images of KEGG pathway maps used to be completely disabled, but now it is partially disabled limiting to those map objects that are used for changing colors in the KEGG mapping procedure. As the result, texts are more readable and illustrations are aesthetically more pleasing.
- The term "Virus ortholog cluster (Voc)" has been changed to "Virus ortholog group (Vog)" in order to distinguish from clusters of positionally correlated genes along the chromosome, such as gene clusters, KO clusters and Vog clusters.
- For each virus gene entry the "Vog cluster" button displays clusters of similar genes along the chromosome of virus genomes.
- The Vog search in the KEGG Virus page now displays those genes that can be assigned Vogs in cellular organisms. Clink on the plus (+) sign in the search result page.
- Another view of gene exchanges between viruses and cellular organisms may be obtained by the traditional ortholog table, which now includes virus genes categorized by the Vtax genomes.
- KEGG pathway map viewer, Brite hierarchy viewer and KEGG genome browser are collectively called KEGG web applications, which are linked from the KEGG top page to describe, especially, pathway map coloring features.
- All types of KEGG pathway map coloring are now performed on the client-side, including the generation of organism-specific pathways (except for global maps which are still processed on the server-side), marking of search results and coloring based on users' data.
- With this change, double-sized png image files, which may be more suitable for publication purposes, may be downloaded from the Download link except for global maps.
- KEGG Genome Browser now allows virus genomes to be handled, especially for searching conserved gene orders using Voc.
- The KEGG Virus ortholog cluster (Voc) dataset is now searchable by keywords, including protein name, virus name, virus family name, Baltimore class and K number, in the KEGG Virus page.
- A new Voc page is also available and is linked from the Voc button of each vg entry page.
- KEGG Genome Browser has been upgraded to enable handling of viral genomes as represented in the NCBI RefSeq data for viruses.
- A new version of BlastKOALA server is released. It uses the dataset of reference genomes and functionally characterized proteins linked from KO references, which is 20 times smaller than the previous non-redundant dataset. The KO assignment algorithm has also been changed (see KO assignment tool).
- A preliminary version of the virus ortholog cluster (voc) dataset is made available for comparison of manually defined KOs and computationally generated sequence similarity groups, such as this. (see KEGG Virus for more details).
- In order to better organize knowledge of gut microbiota metabolism, more specialized datasets are being created, starting with map00946 for degradation of flavonoids and br08012 for dietary phytochemicals.
- In order to meet the needs of higher resolution pathway maps for preparing figures in publication, double (2x) sized image (png) files are available from the Downlod link of each pathway map page.
- The graphical user interface of the KEGG pathway map viewer now allows advanced coloring of map objects including split-coloring and gradation. See details here.
- The KEGG Synteny tool for searching conserved gene clusters is upgraded to allow both fixed and any order of K numbers to be searched automatically. The result can be examined with the KEGG taxonomy browser. The associated tool to start with a given set of reference genomes is also upgraded.
- The KEGG weblinks now include the REST-style URL to launch KEGG Genome Browser, such as https://www.kegg.jp/genome/hsa+59272 or https://www.kegg.jp/genome/T00007.
- In KEGG API, the list operation of KEGG organism code or T number genome identifier has been modified to include chromosomal positions of genes.
- In the pathway map page the Organism menu is reinstated (see map00300, for example) to better understand which organisms in which taxonomic ranks have pathways and modules using the join, pruning, and zoom in/out capabilities of Brite hierarchy viewer.
- The vtax genome page now contains both vg (viral gene) and vp (viral mature peptide) links, such as gn:2697049 for SARS-CoV-2.
- A new tool named KEGG Synteny is released for finding conserved gene orders, or conserved synteny, among KEGG organisms and making local alignments of genomes by the KEGG Genome Browser.
- The vg (viral gene) category of the GENES database is now associated with the viral genome information in the vtax category of the GENOME database.
- A search interface is introduced in the KEGG2 page for searching cited references in the KEGG databases.
- Features of taking snapshots are introduced in the KEGG Genome Browser as an image file (similar to the pathway map viewer) and the current URL (also introduced in the BRITE hierarchy viewer).
- A new tool named KEGG Genome Browser is made available for browsing gene positions and KO annotations in the genome and for searching and comparing similar gene clusters in multiple genomes. See, for example, Homo sapiens and Escherichia coli.
- A hierarchical classification system of drugs is being developed as shown in the Brite hierarchy file for Drug Groups.
- Genome annotation in KEGG has relied on the SSDB database generated by time-consuming SSEARCH computations. A new BLAST-based procedure is in place for assigning KOs to newly released genomes until the SSDB backlog is cleared. This effectively eliminates genomes without annotation.
- The side panel of the pathway map browser now contains ID search and Color (used to be called User data) operations. ID search, Color (for pathway) and Join (for brite) are equivalent to the Search, Color and Join tools of KEGG Mapper.
- KEGG Taxonomy is introduced for linking KOs and modules to taxonomic groups and then to phenotypes.
- A new version of KEGG Mapper is made available. It consists of four basic operations of Reconstruct, Search, Color and Join, and the mapping results of Pathway and Brite hierarchy are linked to new show_pathway and show_brite viewers.
- The JOIN tool has been significantly improved, including the search capability against all available Brite files.
- FDA OTC drug labels are no longer linked from KEGG MEDICUS.
- A new category of the GENES dtabase, vp (viral mature peptides), has been introduced.
- The ENVIRON database, originally introduced as the EDRUG (extension of DRUG) database in 2010 has been discontinued. Main contents have been moved back to the DRUG database.
- The KEGG web pages are being updated together with an attempt to simplify the overall architecture of the KEGG database.
- Rest-style URLs shown in the KEGG WebLinks page are now used in both kegg.jp and genome.jp sites.
- The show_brite viewer for Brite hierarchy files now allows three operations in the left panel: "Search" for text search, "ID search" for mapping a given set of IDs and "Join" for adding columns by combining binary relations.
- Join examples such as in the viral taxonomy and antiinfectives may be examined to understand the concept of Join.
- Brite hierarchy files can now be viewed with the new htext (hierarchical text) viewer "show_brite", which comes with the side panel in a similar manner as the show_pathway viewer for KEGG pathway maps.
- KEGG Mapper is still linked to the previous get_htext viewer for Brite mapping, but this will be replaced by the show_brite viewer.
- KEGG pathway maps and Brite files are better integrated with Related Pathway, Related Brite and Related Brite table links.
- User data mapping option in the pathway map viewer is reinstated as the "User data" operation in the side panel. The new version is a client-side operation and allows user data to be saved in the local storage of the web browser.
- The module list in the side panel of organism-specific pathways now contains the result of completeness evaluation.
- This evaluation has also been incorporated in the Reconstruc Pathway tool of KEGG Mapper, together with the module link mode of global and overview maps.
- The improvements of pathway map viewer (show_pathway tool) started in July are now complete.
- The KEGG NETWORK database has been integrated into the KEGG PATHWAY database. The side panel of the pathway map viewer now contains the network list such as for hsa05210 and hsa05010.
- The viewers of KEGG pathway maps, KEGG modules and BRITE hierarchies (for genes and proteins) now come with "Change pathway type", "Change module type" and "Change brite type" buttons, respectively, to select from reference and organism-specific versions.
- A new virus classification is introduced integrating the ICTV classification and Baltimore classification.
- A new version of the pathway map viewer (show_pathway tool such as for map00010) is implemented with a control panel on the left. The functionality of the left panel will be improved, but currently it contains the scale slider and the search box for all the maps, the module list for metabolic maps, and other features for global/overview maps.
- The module diagrame viewer (show_module tool such as for M00030) shows complete modules in the NCBI taxonomy linked from the Organism menu and the new Module table button.
- The network variation map viewer (show_network tool such as for nt06210) now distinguishes reference networks and variant networks, the latter caused by gene variants, pathogens or environmental factors.
- The global metabolic pathway maps 01100, 01110 and 01120 can now be viewed as consisting of KEGG modules. Choose the module mode to change from KO (or gene) links to module links.
- The KEGG Mapper tool Reconstruct Pathway now contains the result of mapping against the global map 01100 in the module mode, which is shown in the "Module Map" tab.
- The popup menu for organism selection in the pathway map pages now contains only the reference genomes. Use the Organism menu at the top for other genomes.
- A new category of KEGG reference genomes is introduced for those genomes with enough experimental data for gene/protein functions, as seen by the number of sequence links in the pubmed reference fileds of the KO database.
- The KEGG NETWORK database now contains network variants for neurodegenerative diseases.
- The NETWORK search box in the KEGG NETWORK database is linked to a new version of Show Network interface with the Edit mode for moving rows and changing indents.
- In the Japanese version of KEGG MEDICUS search, the data is shown, whenever available, in the format that is compatible with the new instructions for preparing package inserts of prescription drugs.
- KEGG modules have been reorganized, focusing on metabolism and removing redundant data that are available in BRITE hierarchies, such as transporters and two-component systems.
- The dataset of KEGG reaction modules is now treated as part of the KEGG MODULE database.
- A major update of KEGG Mapper is released, where 14 tools have been reorganized into just 3 general tools and 2 specialized tools.
- The most basic tool of Reconstruct Pathway contains new features to search against Brite tables and to check completeness of modules.
- Since mapping against PATHWAY, BRITE and MODULE is now performed simultaneously with the results shown in different tabs, the MODULE database has been reorganized to remove redundancies and to enable completeness check.
- The global map of metabolic pathways has been expanded now containing 50% more KOs and all pathway modules.
- The structures of KEGG GLYCAN may now be displayed with SNFG (Symbol Nomenclature for Glycans).
- The KEGG NETWORK database is being expanded with a new focus on congenital disorders of metabolism. For example, different types of mucopolysaccharidosis are shown in the network variation map nt06012 for glycosaminoglycan degradation.
- The target-based classification of drugs for both English and Japanese versions is associated with the category of drugs, such as monoclonal antibody, gene therapy product and enzyme replacement therapy product.
- KofamKOALA is made available at the GenomeNet site for KO annotation (K number assignment) using HMM profiles.
- In KEGG modules, the pathway module category is made consistent with the KEGG pathway map category.
- In the global and overvew maps (map numbers starting with 011 and 012), each organism-specific pathway is associated with the set of complete modules for the organism. See more details in the help document.
- A new tool, Search NETWORK, is available in KEGG Mapper for search human genes and gene variants in the network variation maps of the KEGG NETWORK database.
- Each KEGG MODULE entry now contains links to module maps of both complete and incomplete modules from the "Organism menu", such as from M00165
- Network variation maps are included in the DBGET system for the NETWORK database, which now consists of N number entries and nt number entries, such as nt06210.
- The category titles of global maps such as "Carbohydrate Metabolism" in map01100 have been removed. Use the option on the left panel to display.
- The no-color (nc) versions of global maps are available for organism-specific maps. Use the size selection pop-up menu.
- Network variation maps in KEGG NETWORK may now include drug-target relationships such as this.
- The search box at the top of KEGG NETWORK may be used to display network variation maps of selected N number entries.
- The Cancer network viewer is linked from Search&Color Pathway tool in KEGG Mapper.
- The ICD-11 codes have been implemented in the KEGG DISEASE database, such as shown here.
- A new category of Virus Network is added to the KEGG NETWORK database.
- The KEGG Orthology (KO) file now contains a complete set of KOs with the classification based on KEGG pathway maps and BRITE hierarchies.
- Web access to www.kegg.jp and www.genome.jp has been changed from HTTP to HTTPS.
- The KEGG NETWORK database now contains endocrine network variants in addition to cancer network variants.
- A new tool is introduced in the KEGG REACTION page for viewing the chemical structure transformation pattern of a reactant pair utilizing the E-zyme software. This tool has been applied to chemical transformations of prodrugs.
- The drug information resource, including the DRUG and DGROUP databases and the BRITE database for drugs is undergoing major changes. Disease information is associated with specific drug products (chemical structures), while target, metabolism and other information is given to chemical structure groups.
- A new search interface is introduced for the NETWORK and VARIANT databases in the KEGG NETWORK page.
- The NETWORK database is also integrated in the KEGG MEDICUS search.
- A collection of virus KOs is officially released. See Viral proteins in the KEGG Virus page.
- The KEGG Pathogen page has been moved from the disease category to the genome category.
- The relationships among disease entries are being reorganized by introducing the subgroup and supergroup names.
- The KEGG NETWORK database is released. It is an attempt to link variations of human genes and genomes to diseases and drugs in terms of variations of networks, such as for signaling networks and transcription networks.
- Reconstruct Brite tool in KEGG Mapper now allows mapping against Brite tables as well as Brite hierarchies. This feature has been incorporated in BlastKOALA automatic annotation server.
- Pathogen Checker tool in KEGG Pathogen has been discontinued because of this enhancement of BlastKOALA.
- A new KEGG Mapper tool, "Draw Phylogram" is released to create a phylogenetic tree from multiple alignment of KEGG GENES and user's sequences.
- Another tool named "Draw dendrogram" is available in the KEGG SSDB database using the SSDB identity score as a similarity measure.
- A flat file representation of the BRITE database is introduced for the DBGET search. It contains only the links to actual BRITE hierarchies and tables.
- A BRITE hierarchy file can now be retrieved in JSON format from the "Download json" link of, for example, br08303.
- The KEGG Mapper "Color Pathway" tool now includes the 3D bar graph option; consequently, the "Color Pathway WebGL" tool is discontinued.
- The KEGG API subscription service is made available at kegg.net.
- The new KO hierarchy file (ko00000) contains a complete set of KOs covering both the KEGG pathway maps (ko00001) and the BRITE hierarchies, as well as the unclassified categories.
- More complete collections of ID mapping data both within KEGG databases and to/from outside databases (see KEGG DB links) are made available in KEGG API and KEGG FTP.
- The top pages of the PATHWAY and BRITE databases are redesigned, the latter now showing all BRITE hierarchy and table files.
- An updated version of KEGG API is released.
- For references in the PATHWAY, MODULE, KO and DISEASE databases, DOI links are included.
- KEGG DRUG entries now contain SIMCOMP field whenever similar chemical structures are present in the DRUG and COMPOUND databases (see, for example, D00293). The list of similar entries can be viewed by clicking on "Neighbor", and a dendrogram can be displayed for selected entries.
- The phylogenetic tree in the KEGG Sequence Data Collection page, such as for beta-lactamase class B, is linked to the taxonomic table, enabling comparison of K number assignments, tree branches and taxonomic compositions.
- KEGG and NCBI genome comparisons are made for both eukaryotes and prokaryotes in the KEGG GENOME page.
- A new interface for the KEGG sequence data collection is released together with FASTA sequence files and phylogenetic analysis results.
- The copyright permission request form has been separated from the feedback form in order to expedite the processing.
- The output format of the GENES entry list, such as in the DBGET keyword search result and the KEGG API list operation, has been modified, indicating the KEGG annotation (KO assignment) first, followed by the annotation of original databases.
- Upon request BlastKOALA software is made freely available to users with KEGG FTP subscription for organizational use. Please use the feedback form to make a request.
- The Convert ID tool for conversion of outside IDs to KEGG IDs is included in KEGG Mapper.
- The phylogenetic tree such as for antimicrobial resistance genes now allows coloring of branches based on the assigned KOs. SSDB ortholog and paralog search results may also be viewed in a similar way using the Create dendrogram menu.
- Subject-oriented entry points to the KEGG resource are introduced in the KEGG top page, including KEGG Virus and KEGG Plant.
- The phylogenetic tree viewer now allows coloring of branches based on assigned KOs, such as for beta-lactamase class A.
- The KEGG RPAIR database has been discontinued. Note that its main content continues to be available as reactant pairs represented by C number pairs in the KEGG RCLASS database.
- The KEGG DGENES database has been discontinued.
- The plasmids category of KEGG GENES has been removed.
- A new page for selected viruses is added.
- A new tool, Search Disease, is available in KEGG Mapper. Given a set of human genes or KOs it reports KEGG DISEASE entries containing matching disease genes.
- KEGG DGENES will be discontinued on October 1 (Release 80.0), since most of the genomes in this draft category have been moved to the GENES database.
- The Plasmids (pg) category of the GENES database will also be discontinued on October 1. Plasmid genes that are not represented in KEGG organisms are incorporated, whenever necessary, in the Addendum (ag) category.
- As announced all non-main type reactant pairs have been suppressed in the KEGG RPAIR database.
- Each KEGG RCLASS entry is now associated with a collection of reactant pair image files showing chemical transformation patterns.
- The NCBI virus taxonomy is added in the Map Taxonomy tool, and also as the "Virus taxonomy" button in the KO page containing viral genes.
- Pharmacologic class information represented by the KEGG DRUG database is included in KEGG DRUG and KEGG DGROUP entries.
- Selected viral genome entries with relevance to diseases are added to the KEGG GENOME database. While T40000 represents viral taxonomy as a whole in the KEGG GENES database, additional T4 numbers (such as T40048) represent specific viral taxonomic categories that are linked from KEGG DISEASE entries.
- The Pathogen Checker tool is officially released. It searches against a dataset of antimicrobial resistance genes.
- The Join Brite Table tool is released in KEGG Mapper. It is a variant of the Join Brite tool, adding a user-defined column to a Brite table file.
- KEGG ENZYME, which now contains manually identified sequence data for EC numbers, is linked from the top page.
- The AMR gene collection, such as for beta-lactamases, is associated with FASTA sequence data files and phylogenetic tree files.
- An updated tool of drug interaction checker is released in the Japanese version of KEGG MEDICUS.
- A new version of link and conv operations is released in KEGG API. In contrast to the previous version that depended on LinkDB at GenomeNet, the new version is more up-to-date and runs faster.
- The KEGG GENES addendum category has removed the restriction of complete genomes when defining KOs, which has enabled the KO database to incorporate all functionally characterized proteins. Currently there are three focused areas: proteins in the KEGG pathway maps that have not been linked to GENES, anitimicrobial resistance (AMR) genes and protein sequence data for Enzyme Nomenclature.
- AMR genes are made available in the KEGG Pathogen page, while the effort to associate sequence data to Enzyme Nomenclature is described in the new KEGG Enzyme page.
- A new mapping operation, named "Join Brite Table", is introduced for combining a BRITE table file and a binary relation file, which effectively adds a column to the table. This is implemented together with "Join Brite" for a Brite hierarchy file in the Drug Classification.
- Following the addition of plasmids, viruses and addendum categories in KEGG GENES, the main category of KEGG organisms is expanded. The restriction of completely sequenced genomes for prokaryotes has been removed to incorporate phylogenetically important genomes. A comparison of KEGG organisms and NCBI reference/representative genomes is shown here.
- The NCBI-GI option was removed from the ID conversion interfaces in KEGG GENES, KEGG Mapper and KEGG API.
- NCBI GI links from KEGG GENES are being changed to ProteinID (INSDC protein accession) links because of the NCBI's announcement to eliminate GI's next year. NCBI GeneID links will remain available for eukaryotes, a small number of reference genomes in prokaryotes, viruses and plasmids, but not for most other prokaryotic genomes.
- KEGG GENES is a collection of complete genomes (each identified by the organism code or T number), but it also includes the Plasmids (pg or T20000) and Viruses (vg or T40000) categories introduced in Release 73.1 and now a new category named Addendum (ag or T10000) for a publication-based collection of functionally characterized genes.
- Taxonomy mapping, such as from a KO page, has been changed from the KEGG taxonomy to the NCBI taxonomy, which now includes the pg, vg and ag categories identified by the NCBI taxonomy IDs.
- In addition to the existing BlastKOALA server, a new server called GhostKOALA has been released. The new server is suitable for annotating a large amount of metagenome sequence data.
- A preliminary version of Pathogen Checker tool is released. It is a specialized version of BlastKOALA for inferring drug resistance and other phenotypic features from pathogen genomes.
- The Module Table tool for examining taxonomic distribution of KEGG modules and KO entries has been upgraded to correctly include plasmid (pg) entries.
- The collections of viruses and plasmids from RefSeq are included in the KEGG GENES database with K number annotations.
- The previous unannotated collection of viruses in KEGG VGENES and VGENOME has been discontinued.
- The KEGG Annotation page is upgraded and linked from the top page. It now contains a new tool, Module Table, for examining taxonomic distributions of KEGG modules and KO entries.
- The KEGG DGROUP database is being associated, when possible, with structural information such as in DG01458.
- A new KEGG Mapper tool, Annotate Sequence, is made available using the BlastKOALA server.
- BlastKOALA has been enhanced to allow examination of GFIT data (BLAST hits) for verification of automatically assigned K numbers.
- An updated version of the KEGG/GenomeNet feedback form is available both at the kegg.jp site and the genome.jp site.
- Reaction module data (html files) are included in the FTP distribution.
- The color coding for the KEGG ORTHOLOGY background color is changed from #edddcd to #f2e9b6.
- BlastKOALA, a new service for genome/metagenome annotation, is released.
- A new database, KEGG DGROUP for drug groups, is released.
- The search box found at the top of KEGG DISEASE and DRUG pages now returns a simultaneous search result against DISEASE, DGROUP, DRUG, ENVIRON, and COMPOUND.
- The KEGG Annotation page is released. It contains KEGG taxonomy checker for checking the organism groups assigned to KEGG modules and KO groups, and KEGG annotation guide to help distinguish related modules and complexes.
- Genus and species information of KEGG organisms is now clearly defined.
- RDF (Turtle and N-Triples) format is supported in link and conv operations of KEGG API.
- KEGG GENES is generated from NCBI RefSeq now using assembly IDs rather than bioproject IDs.
- An updated version of Color Pathway WebGL (formerly, Color Pathway 3D) tool is available in KEGG Mapper. The KEGG Atlas cancer map viewer has also been updated.
- The ddi (drug-drug interaction) search operation in KEGG MEDICUS API now accepts FDA's National Drug Codes (NDCs).
- KEGG EGENES and EGENOME for EST datasets are discontinued.
- A new version of Map Taxonomy tool is introduced in KEGG Mapper. It enables to examine the organism groups assigned to a KEGG Orthology group (K number) or a KEGG module (M number).
- The KEGG DISEASE, DRUG and ENVIRON databases are moved to the Health Information Category, and the changes are made in the ordering of KEGG databases (such as in KEGG2) and BRITE hierarchy files (such as in BRITE).
- KEGG EGENES for EST datasets will be discontinued in the next release.
- The KEGG MEDICUS Drug Interaction Checker is available for drug products in the USA.
- The completeness check mechanism has been introduced in the KEGG MODULE database, showing which organisms or organism groups have complete modules or incomplete but almost complete modules.
- The KEGG Mapper tool Reconstruct Module also includes an option to select complete and incomplete modules.
- The KEGG MODULE M number, especially for a signature module, may now be defined as a combination of both K numbers and other M numbers.
- The global maps (map numbers 01100s) and the overview maps (map numbers 01200s) of KEGG metabolic pathways contain manually entered coordinates for KEGG modules, and the overview maps contain those for reaction modules as well. The show_pathway routine now handles KEGG modules and reaction modules, such as for map01210.
- In the metabolism section of the KEGG PATHWAY database, the first category is now called "Global and overview maps" consisting of map numbers 01100s and 01200s, which are tightly integrated with KEGG modules and KEGG reaction modules. Note that the reaction module maps category is merged into this category.
- A new version of KEGG Atlas is released to handle KEGG modules and reaction modules in these maps.
- The pathway map HTML pages are no longer statically generated. The URL such as /kegg/pathway/map/map00010.html will continue to be supported, but some old CGI programs that utilize static files do not work any longer. It is recommended to use "show_pathway" rather than "mark_pathway_www" for pathway map coloring (see KEGG WebLinks).
- KEGG MEDICUS API, an addendum to KEGG API, is released. It allows handling of drug products marketed in Japan and the USA.
- KEGG BRITE now contains html table files, such as for pharmacogenomic biomarkers.
- KEGG reaction modules now contain variation patterns and combination patterns.
- A new metabolic pathway category, "Reaction module maps", is introduces. It contains pathway maps describing connection patterns of reaction modules.
- The pathway category name "Overview" is changed to "Chemical structure transformation maps".
- KEGG ENVIRON now contains an interface to environmental pollutants and other health-damaging substances stored in the KEGG COMPOUND database.
- As announced six months ago, the SOAP API service was terminated at the end of 2012.
- A new dataset of KEGG reaction modules is released.
- KEGG DRUG now contains an interface to check a given set of drugs (D numbers) for any interactions associated with contraindications and precautions as described in the drug labels.
- In the Japanese version of KEGG MEDICUS, this search can be performed for individual products (rather than D numbers).
- The new REST-style version of KEGG API is released, together with an updated version of KEGG web links.
- The KEGG organism code for the GENES database is no longer limited to three letters. Some may consist of four letters.
- New "Reconstruct Pathway/Brite/Module" tools are made available in KEGG Mapper helping genome and metagenome annotations.
- Another mapping tool, "Color Pathway 3D", is linked directly to KEGG Atlas 3D viewer.
- "KEGG MEDICUS My Medication List" is released (Japanese version only).
- The KEGG MEDICUS search now integrates FDA drug labels for both prescription and OTC drugs.
- The search box in the KEGG top pages includes an option to select from KEGG search, DBGET search, and MEDICUS search.
- A composite database named GENOMES is created consisting of GENOME for complete genomes in GENES and DGENES, EGENOME for EST datasets in EGENES, and MGENOME for environmental samples in MGENES.
- As of December 19, 2011 the KEGG database development was separated from the GenomeNet service. The KEGG team is responsible for the development of the 17 databases listed in the KEGG overview page. MGENES and EGENES as well as MGENOME and EGENOME are GenomeNet extensions of KEGG.
- KEGG MEDICUS allows an integrated search against KEGG PATHWAY, KEGG DISEASE, and KEGG DRUG.
- The Japanese version of KEGG MEDICUS allows an integrated search with package insert information of all prescription drugs and OTC drugs marketed in Japan.
- The 3D map viewer linked from the new portal KEGG Cancer is integrated in KEGG Atlas.
- KEGG Mapper now includes mapping tools for KEGG MODULE in addition to KEGG PATHWAY and KEGG BRITE.
- A preliminary version of 3D map viewer is released and linked from the KEGG MEDICUS page.
- KEGG FTP subscription is introduced.
- The Color Pathway tool of KEGG Mapper now accepts numerical data, which can be displayed by gradation and optionally by 3D representation as well.
- An enhanced version of KEGG Mapper is released.
- KEGG pathway maps indicating disease genes and drug targets are now treated as a special class of organism specific pathways with the organism code "hsadd".
- This extension is also applied to organism specific BRITE hierarchies.
- In a similar way, extended versions of ATC and other drug classification systems with target and metabolizing enzyme information are made available.
- An enhanced version of KEGG MODULE is released containing computationally generated module maps, allowing KEGG module mapping similar to KEGG pathway mapping.
- KEGG MEDICUS contains a collection of human pathway maps with known disease genes and drug targets marked in different colors, which can be used in the "Search Pathway" tool of KEGG Mapper.
- Newly developed xenobiotics degradation pathway maps have been released.
- KEGG MEDICUS is introduced as an interface to KEGG pathway maps containing disease genes and drug targets.
- Disease/drug mapping and user data mapping links are added to KEGG pathway maps.
- KEGG pathway mapping capabilities are enhanced for the display of combined pathways, for example, for human and gut microbiome.
- Tab-delimited fields are better handled in the BRITE functional hierarchy files, including the JOIN operation of a BRITE file and a binary relation file.
- The collection of KEGG PATHWAY and BRITE mapping tools is now called KEGG Mapper.
- A new database of reaction class, KEGG RCLASS, is released for the grouping of similar reactions on the KEGG pathway maps, based on the RDM patterns of main reactant pairs.
- A drug extension (or extra) database, KEGG EDRUG, is released containing crude drugs and other plant natural products, distinguishing from the collection of approved drugs in KEGG DRUG.
- KEGG PLANT is discontinued and merged into KEGG EDRUG.
- An updated version of KEGG Atlas now handles the global maps with layer information such as pathway modules.
- An updated version of show_organism interface now handles dynamically generated maps for DGENES/EGENES/MGENES in a similar way as those for GENES.
- The KGML+ (KGML+SVG) file for the global metabolism map (map01100) is released at the ftp site.
- KEGG GENOME now contains metagenomes for environmental samples, together with the gene catalog KEGG MGENES.
- Multiple strains may be combined to define a pangenome; more generally an organism group may be defined as any combination of KEGG organisms.
- Organism-specific pathway maps for draft genomes (DGENES), EST datasets (EGENES), and metagenomes (MGENES) are dynamically generated (no static maps are available at the ftp site).
- Combined pathway maps may also be generated dynamically for pangenomes and organism groups based on the curated KO assignment for GENES.
- Metabolic pathway map categories have been changed. "Biosynthesis of Polyketides and Terpenoids" and "Biosynthesis of Secondary Metabolites" are reclassified into "Biosynthesis of Polyketides and Terpenoids" and "Biosynthesis of Other Secondary Metabolites".
- KEGG DISEASE database is available for download at the FTP site.
- The KEGG Orthology system now contains the categories of both KEGG pathway maps and BRITE functional hierarchies.
- Each KEGG entry is now displayed together with "All links" information, which is obtained from the GenomeNet LinkDB database.
- New tools are available for mapping against BRITE hierarchies and KEGG taxonomy trees.
- A new pathway search facility is introduced enabling keyword search against pathway title, description, free text in the map, etc.
- The XML files for the KEGG pathway maps are made available at the FTP site in both the original KGML format and the converted BioPAX level 2 format.
- KEGG OC (Ortholog Clusters) is made available at the FTP site, containing orotholog clusters computationally generated from the KEGG SSDB database.
- The image maps of KEGG PATHWAY have been changed from GIF to PNG.
- A search box is introduced to each pathway map, where pop-up texts on top of the pathway objects are searchable.
- The pathway search and mapping tools now include the global metabolism map as well.
- KEGG DRUG is moved from the LIGAND category to the new MEDICUS category.
- The read-only version of KEGG annotation tools, KOALA and GFIT, can now be viewed from the KO and GENES entry pages.
- Global metabolism map is implemented with the traditional image map viewer.
- A new tool to generate a taxonomy tree from a set of NCBI taxonomy IDs is released.
- REST based URLs for retrieving KEGG entries and pathway maps are made available at the kegg.jp site.
- All the KEGG pathway maps have been redrawn with the KegSketch tool to generate KGML+ (KGML+SVG) files.
- KEGG Atlas is completely redesigned and now based on the KGML+ files.
- The traditional pathway map viewer using GIF image files is upgraded with the zooming capability.
- KEGG PLANT is released as a new resource for plant genomes, secondary metabolism, and natural products.
- The KEGG ORTHOLOGY (KO) system is explained in a new page together with the KEGG annotation procedure.
- An interface to process KEGG object identifiers is added at the top of the main pages.
- The KEGG PATHWAY database now contains, in addition to the graphical pathway maps, text-based pathway entries for description of biological processes shown in the pathway map, lists of genes and molecules that constitute the pathway, and associated reference information.
- KEGG DGENES is merged into KEGG GENES.
- A new version of KEGG Atlas viewer is released using the <canvas> element.
- Subcategorization of KEGG DRUG entries is introduced distinguishing mixtures, crude drugs, and TCM (Traditional Chinese Medicine) formulas.
- The KEGG Atlas cancer map is released combining 14 existing cancer pathway maps.
- The new GECS (gene expression to chemical structure) software is released, currently, for prediction of N-glycan structures from microarray gene expression profiles.
- The global map of KEGG metabolic pathways is released as the first component of KEGG Atlas.
- Smaller units of existing KEGG pathways are now stored in the KEGG MODULE database, which also contains other functional units of pathways and complexes.
- The KEGG DISEASE database is released containing gene/molecule lists for selected diseases.
- A new page, KEGG COMPOUND, is prepared for pathway-based reorganization of biochemical compounds.
- KEGG EGENES, which is constructed from massive EST libraries, now incorporates singletons as well as contigs.
- The Organism subfield is introduced in KEGG ENZYME for the organism information manually taken from the original references.
- The Structure field is introduced in KEGG GENES containing cross-reference links from GENES to PDB refined by the corresponding organism information.
- Java Web Start is introduced for launching KegTools: BRITE to KegHier, COMPOUND/GLYCAN to KegDraw, and EXPRESSION to KegArray.
- Peptide entries in the COMPOUND database now contain the SEQUENCE field, similar to PK/NRP entries.
- New version of the hierarchical text file viewer "get_htext" is released.
- PK/NRP entries are added to the COMPOUND database with the new SEQUENCE field.
- Server-side viewer is discontinued for the EXPRESSION database, which is now linked to KegArray.
- New directory organization of the FTP site.
- New search box is introduced in the KEGG top page.
- The entire text of all BRITE files can now be searched with keywords.
- Reactions subcategory in the BRITE database.
- RPAIR database updated to reflect most of the KEGG reactions.
- The Japanese language interface to the KEGG system is released.
- KEGG update notes in RSS feeds.
- The mapping to BRITE hierarchies is implemented as an operation to combine two files: a binary relation file and a hierarchical text file.
- Ortholog group tables to be discontinued.
- KEGG pathway modules released.
- New top page for KEGG SSDB.
- DBGET implementation of KEGG BRITE.
- Standalone java application KegHier for accessing and handling BRITE files.
- Automatic conversion of outside database identifiers is implemented. Gene/protein identifiers such as in NCBI RefSeq (Entrez Gene) and UniProt can now be directly used in KEGG GENES.
- A new category of the KEGG PATHWAY database "Drug Development" is made available. It is a collection of KEGG DRUG structure maps illustrating our knowledge on drug development.
- Manually drawn glycan structures are included in the Glycan section of the KEGG PATHWAY database to supplement computationally generated Composite Structure Map (CSM).
- The LIGAND relational database (primary) version of KEGG DRUG is made available in addition to the DBGET (secondary) version.
- The KEGG REACTION data is enhanced with the introduction of the categorization of chemical structure transformation patterns, called RDM patterns, in the RPAIR database.
- A new interface is introduced to DRUG, GLYCAN, REACTION, EXPRESSION, and Auto Annotation (KAAS).
- KEGG automatic annotation server, named KAAS, is released to assist annotation (KO assignment) and KEGG pathway mapping of newly determined genomes.
- Cross-reference lists are made available for conversion of IDs between KEGG and outside databases.
- KEGG DRUG is introduced separating from KEGG COMPOUND to accumulate chemical structures, therapeutic categories, targets, and other information of drugs.
- Different entry points are prepared for accessing KEGG, called Generalized KEGG, Specialized KEGG, and Personalized KEGG in the KEGG2 (table of contents) page.
- One feature of Specialized KEGG is an organism-specific view of KEGG.
- Another feature is customization of KEGG organism menu used to display pathway maps, etc. Cookie must be enabled to make this feature to work.
- By making use of the LinkDB resource in GenomeNet, KEGG pathways are linked to many different outside databases, such as NCBI Entrez and UniProt.
- Automatic annotation and pathway mapping of draft genomes (DGENES) and EST consensus contigs (EGENES) are released, which significantly increased the number of KEGG Organisms.
- KEGG BRITE is officially introduced as the fourth component of KEGG, providing among others classifications of drugs and compounds.
- KegDraw for drawing chemical compound and glycan structures is released.
- A new glycomics resource "KEGG GLYCAN Composite Structure Map" is released. Genes in the genome or the transcriptome can be mapped on a composite structure generated from the GLYCAN database so that organism-specific or expressed glycan structures can be viewed and examined.
- A high-level KEGG pathway map is introduced for an overview of biosynthetic pathways. Such high-level maps will be used in the future for computational inference in the BRITE database.
- A therapeutic category of drugs in the COMPOUND database is released based on the Japanese Pharmacopoeia.
- A preliminary version of EGENES, a collection of plant EST contigs, is released. Currently it contains no annotation, but in a future release KEGG pathways will be generated by automatic KO assignments.
- The Oracle version of the LIGAND database is released replacing the ISIS version.
- New in-house programs SIMCOMP and SUBCOMP can now be used for searching similar compound structures against the COMPOUND or REACTION database.
- Another new program e-zyme has been developed to predict reactions between given compound pairs with assignments of possible EC numbers.
- The RPAIR database is released as part of LIGAND, containing the reactant pairs that constitute enzymatic reactions with information about atomic alignments.
- The DBGET entries of the KEGG databases are shown in a nicer view with buttons to link other KEGG resources and help messages.
- The GFIT tables that have been used for genome annotations are incorporated into the SSDB database (Oracle), which makes the gene cluster search much faster than before.
- KGML v0.4 contains a major restructuring of elements.
- A preliminary version of KegArray, a Java application for microarray data analysis, is released for Mac OS X.
- The KEGG pathways are linked again to human diseases genes in the OMIM database.
- New user interfaces are introduced to reflect the basic structure of KEGG. Conceptually, KEGG consists of three graph objects called the protein network (PATHWAY database), the gene universe (GENES/SSDB database), and the chemical universe (LIGAND database).
- The Java applet version of KEGG genome map browser is discontinued. It is replaced by a new version using dynamically generated image maps.
- The Java applet version of KEGG expression browser will also be discontinued.
- The automatic generation of ortholog group tables incorporates coloring of gene clusters.
- KGML v0.3 comes with part of KEGG regulatory pathways.
- The GLYCAN database is released as a new effort to collect complex carbohydrate structures. GLYCAN is part of the DBGET system and the structure search is available together with the Java-based input tool.
- CarbBank is also implemented in the DBGET system.
- The first release of KEGG API is made available. It is a SOAP interface suitable for automating access to and use of KEGG.
- KGML (KEGG Markup Language) v0.2 is available with reaction data in metabolic pathways.
- The results of computationally generated ortholog and paralog groups in SSDB can now be viewed by the adjacency matrix viewer.
- An XML version of the KEGG metabolic pathways is made available in the KGML (KEGG Markup Language) v0.1.
- KO (KEGG Orthology) is officially released in the following: KO database in DBGET, KO entries linked to SSDB clustering, and 'all organisms' pathways linked to KO.
- The reference metabolic pathways are now of two types: those linked to enzymes (EC numbers) and those linked to KEGG reactions (R numbers).
- The GENES and SSDB databases are operational on Oracle.
- SSDB now contains TIGRFAMs in addition to Pfam and Prosite.
- REACTION database is made available in DBGET.
- The fifth top category of "Human Diseases" is introduced in the hierarchy of KEGG pathways.
- The top category of "Cellular Processes" is also being reorganized.
- The hierarchy of KEGG pathways is now called KO (KEGG Orthology). The KO identifiers will be introduced shortly.
- Automatic generation of ortholog group tables using the "select organism" option.
- The Chemscape version of the LIGAND database is released, enabling substructure searches against COMPOUND and REACTION databases.
- The Java-based dendrogram viewer is implemented in both the Expression database and the SSDB database.
- The KEGG Expression Database contains an increasing amount of microarray gene expression profile data for Synechocystis PCC6803 and Bacillus subtilis, together with an enhanced version of KEGG expression browser.
- The initial phase of SSEARCH computation for all pairwise genome comparisons has been completed in the SSDB Database. The result of cluster analysis can now be examined with a Java dendrogram viewer.
- A new database named SSDB is implemented. It contains similarity scores of all gene pairs in the GENES database computed by SSEARCH at the amino acid sequence level. It also contains the information about best hits and double-best hits when two genomes are compared.
- A hierarchy of organism groups in the KEGG menu page and associated DBGET search.
- A hierarchy of genes in the list of ortholog identifiers, which is used for automatic matching of genes in the genome and gene products in the pathway.
- The database name GENOMES is changed to GENOME, which now represents both the information about individual organisms and the collection of Java genome maps.
- The cell lineage of H.roretzi is now represented by a graphical image map, which is linked to actual pictures of early-stage embryo.
- Different types of analysis tools for microarray expression data are being integrated into a single interface of KEGG expression database.
- The gene catalog search is incorporated in the DBGET/LinkDB system as the hfind mode.
- A new version of expression browser is implemented.
- The MOTIF search can now be automatically invoked from any GENES database entry.
- The KEGG metabolic pathway section now includes pathways of the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD).
- The ortholog IDs are introduced as an extension of the EC numbers for matching the pathway information with the genomic information, such as for automatic generation of organism-specific pathways.
- As a result of this extension, KEGG metabolic pathways may now contain gene names.
- The get_htext program to handle hierarchical text data, such as gene catalogs, has been upgraded. It now runs ten times faster and supports more options.
- Introduced the GENOMES database for a collection of completely sequenced genomes.
- Enhancements of the expression map browsers including the new tool.
- A new type of hierarchical text data is introduced for browsing cell lineage maps.
- FASTA search against GENES database can now be performed both at the amino acid and nucleotide sequence levels.
- A preliminary version of expression map browser is made available for analyzing microarray gene expression data.
- The table of contents page is reorganized.
- The regulatory pathways page is reorganized.
- In the ortholog group tables, the column-wise extraction of gene definitions is now possible in addition to the row-wise extraction.
- An entry in the GENES database can now be retrieved in the DBGET/LinkDB system either by the gene accession (such as b1882 or YAL041W) or by the primary gene name (such as cheY or CDC24).
- A new version of genome map browser has been implemented. The browser now has two windows: an HTML window and a Java window. The HTML window contains the overall map in Java, which integrates both linear and circular chromosomes, and also incorporates plasmids and extra chromosomal elements. The Java window is an enlarged window around the position specified in the overall map, which now displays five lines by default.
- It has become possible to color genome maps and ortholog group tables, in addition to pathway maps, for distinguishing different groups of genes such as in the gene expression profile experiments.
- An effort to classify chemical compounds is initiated.
- The objects in the KEGG pathways can now be marked by any combination of colors, which should be useful in coloring genes according to the expression profiles obtained by microarray or DNA chip experiments.
- The KEGG mirror server package has been released.
- The genome map browser has a new interface that runs much faster than the previous version.
- A new capability to compare two genome maps has been implemented. It is a 'dot matrix' of similar genes that can be used to identify clusters of genes that share sequence similarities.
- The GENES amino acid sequences and the whole GENOME nucleotide sequences can now be searched by both FASTA and BLAST either from the KEGG table of contents page or the KEGG tools page.
- A new category of ortholog/paralog group tables is added to the KEGG pathway section.
- A prediction tool is made available for gene function assignment by searching sequence similarities and by making use of the information of a functional unit in the ortholog/paralog tables.
- Started providing a suite of genome map comparison tools, including the search for homologous gene clusters.
- Genome map search - A new capability to search genome maps for gene positions is released.
- Pathway map search - The capabilities to search pathway maps for enzymes, compounds, and genes are combined in a single user interface under the WWW version, which is now consistent with the e-mail version.
- In the result of path computation program PathComp, the user can now examine a series of compound structures to select plausible pathways.
- Started organizing molecular assemblies which are tentatively classified under the regulatory pathway section.
- Started organizing different types of molecular catalogs, especially for human proteins.
- The compound data has been fully integrated. A circle on the pathway diagram is now a clickable and searchable object.
- All image maps are now handled at client side, which enables easy recognition of clickable area by the cursor.
- The gene catalog for each organism now contains the classification of regulatory pathways.
- The pathway search routines by EC numbers, compound numbers, and gene names can now be used as an e-mail server. The address is: pathway@genome.ad.jp.
- A set of gene names of a given organism can be used as a query to search matching names on the KEGG pathways.
- A set of amino acid sequences can be used as a query to search similar sequences on the KEGG pathways, which will be especially useful in pathway reconstruction.
- KEGG Release 3.1 contains a new collection of regulatory pathways, in addition to the previous collection of metabolic pathways.
- The KEGG TOC page is non-framed.
- This is the first official CD printing. The previous ones were made in-house.
CD Release 2.1, May 1, 1997
- The KEGG TOC page is framed.
- New Java launchers are installed.
CD Release 2.0, April 3, 1997
- The Internet version relies less on Java making it more widely available.
- The CD version experiments a number of advanced features of Java and Javascript which may only be appreciated by Netscape 3.01 or later.
- The weekly updated CD version of KEGG may be downloaded by anonymous FTP.
CD Release 1.1, December 27, 1996
- The Java option of KEGG is now fully implemented.
- The first official release of KEGG contains five organisms, Haemophilus, Mycoplasma, Methanococcus, Synechocystis, and Yeast.
- A new program, ec_point, is released for searching enzymes on the metabolic pathways.
- Genome browsers, ZoomDial for circular genomes and ZoomLine for linear genomes, are released.
- The clickable chromosome maps are available for accessing GDB and OMIM data.
- The enzyme classification according to PROSITE patterns is added.
- The metabolic pathway data are being verified with different sources and modified accordingly.
- The pathway data for most of the known metabolic pathways have been entered and properly classified. They may now be accessed through a clickable diagram.
- The genes tables are available for 13 species and human disease genes.
- It is now possible to identify enzymes that appear in OMIM, PDB, and PIR databases. Click the title box in each pathway diagram.
- To assist enzyme search against the pathway diagrams, a new window is added for EC number search.
- A bare backbone of KEGG is available consisting of gene classification tables for selected organisms, three types of enzyme classification tables, and a selected number of metabolic pathway diagrams.
- The basic capabilities of hierarchical text handling and graphics diagram handling are available.
- The search capabilities include key word search on a hierarchical text and enzyme (boxed object) search on pathway diagrams.
- A repertoire of enzyme genes in each category may be identified on the corresponding pathway diagram. Click the link marked MAP in the gene classification table.