Announcement: Minor update of KEGG API
Starting on March 1, 2023 the list operation of KEGG API returns KEGG identifiers without the database name in most cases, in compatible with the form shown in Figure 1 of the recent
NAR article.
Posted on February 20, 2023
Announcement: Field name changes in KEGG Database Entry Format
The database entry field names of NAME and DEFINITION have been used somewhat differently in the KO, GENES and GENOME databases. In order to make these databases compatible with other databases, the DEFINITION field is now called the NAME field, and the previous NAME field is called either the SYMBOL field (KO and GENES) or the ORG_CODE field (GENOME).
Posted on September 21, 2021
KEGG ENVIRON to be discontinued
As an attempt to simplify the overall architecture of the KEGG database, the contents of
KEGG ENVIRON are being merged into KEGG DRUG or KEGG COMPOUND.
Posted on April 9, 2021
Announcement: Module mode of global matabolic pathway map
The global metabolic pathway map can now be viewed as consisting of KEGG modules in the module mode. This mode is implemented in the Reconstruct Pathway tool of KEGG Mapper.
Posted on June 1, 2020
Announcement: Major changes of KEGG MODULE
The KEGG MODULE database is undergoing major changes to focus on metabolic pathways.
- Non-metabolic pathway modules and molecular complexes are removed. Essentially the same data have been available in the KEGG BRITE database, and the Reconstruct Pathway tool of KEGG Mapper may be used for completeness check.
- Reaction modules identified by RM numbers are incorporated into the MODULE flat file for use by the DBGET search system. The actual contents of reaction modules continue to be available as html files.
- The MODULE flat file no longer contains organism-specific versions of complete modules. All modules, complete or incomplete and reference or organism-specific, continue to be available in the module map (show_module) interface.
Posted on September 12, 2019
ICD-11 codes implemented in KEGG DISEASE
ICD-11 (International Classification of Deseases 11th Revision) was released by WHO on June 18, 2018. Accordingly, ICD-11 codes have been implemented in the
KEGG DISEASE database. Currently both ICD-11 and ICD-10 are shown in each disease entry, but ICD-10 will be removed by the end of 2018.
Posted on August 1, 2018
Announcement: New Brite file for KEGG Orthology (KO)
In the next release 87.0 on July 1, 2018 the format of the Brite file for "KEGG Orthology (KO)" will change. Please start using "KEGG Orthology (KO) - All Categories", which will be the new "KEGG Orthology (KO)" file. The content of the current version (pathway maps only) can be reproduced by removing the branches of 09180 and 09190.
Posted on May 24, 2018
Announcement: HTTPS at www.kegg.jp
The KEGG main website at www.kegg.jp is moving from HTTP to HTTPS. On and after June 1, 2018 all traffick
to
http://www.kegg.jp
will be automatically forwarded to
https://www.kegg.jp. The KEGG mirror site at www.genome.jp/kegg/ will also move to HTTPS on the same date. Note, however, that KEGG API at rest.kegg.jp will remain HTTP.
Posted on April 23, 2018
Updated on June 23, 2018
Announcement: KEGG NETWORK released
The KEGG database was first made available on December 1, 1995. After 22 years we chose the same date to release
KEGG NETWORK, a new database for linking human genomes to diseases and drugs in terms of network variation. The basic idea is presented in the network variation map, such as shown
here.
Posted on December 1, 2017
Announcement: KEGG API for non-academic users
In order to promote wider usage of KEGG in real-world applications, the KEGG API subscription service is made available at
kegg.net. In contrast to the existing
KEGG API service, which is limited to academic users, this new service is intended for commercial users developing and maintaining products, such as application programs and data analysis services.
Posted on August 1, 2017
Announcement: KEGG RPAIR to be discontinued
The
KEGG RPAIR database has been developed as a comprehensive collection of chemical structure transformation patterns, called RDM patterns, for substrate-product pairs of all reactions stored in the KEGG REACTION database. Internally only the RDM patterns of "main" pairs are then used to define reaction classes in the KEGG RCLASS database. The collection of reaction classes has turned out to be useful for annotating enzyme genes by the KEGG Orthology (KO) system (see
KEGG Reaction Modules) and we focus on improving the RCLASS database. Because defining RDM patterns requires extensive manual work, we will select reactant pairs and reaction classes that are relevant for this improvement. We will no longer assign RDM patterns for all pairs, nor define reaction classes for all unique RDM patterns of main pairs.
The scheduled changes of the KEGG RPAIR database are as follows.
- We have already stopped creating non-main type reactant pair entries.
- On July 1, 2016 we will suppress all existing non-main type reactant pair entries.
- On October 1, 2016 the KEGG RPAIR database will be discontinued.
Please note that the essential content of the RPAIR database will continue to be available in the RCLASS database. We simply eliminate RP number identifers (eg.,
RP04458) and use equivalent C number pair identifiers (eg., C00025_C00624).
Posted on May 18, 2016
Notice to KEGG API users: conv and link problems
Since around August 21, the update of the LinkDB database at GenomeNet has become unstable due to the huge increase of the data size. As the result, the conv and link operations of KEGG API sometimes do not return any result.
We are working on a new method that does not depend on LinkDB.
In the meantime please report any problems through the
KEGG/GenomeNet feedback form.
Posted on September 22, 2015
A new version of link and conv operations is released.
This version does not include indirect links that were computationally generated in LinkDB, such as:
/link/cpd/hsa
which no longer works. Instead, please use the combination of:
/link/ko/hsa
/link/rn/ko
/link/cpd/rn
Posted on February 1, 2016
Updated on February 24, 2016
Announcement: Data Source of KEGG GENES
The KEGG GENES database for prokaryotic genomes was created using the RefSeq FTP site until January 2014 or until it was updated. Since then newly added prokaryotic genomes are all taken from GenBank.
The NCBI has recently released updated prokaryotic RefSeq genomes annotated by the NCBI Prokaryotic Genome Annotation Pipeline. Consequently, gene assignments and locus_tags are different from current KEGG data, and RefSeq annotation now contains WP_ records for cross-species identical sequences.
Excluding the RefSeq reference genomes (currently 122 genomes) that are annotated manually, all prokaryotic genomes previously taken from RefSeq are being updated with GenBank as the data source. Note that eukaryotic genomes will continue to be taken from RefSeq, as well as viruses and plasmids, as summarized in the table.
Together with this change, all protein coding genes are associated with NCBI Protein IDs (INSDC accessions) and GI numbers are being eliminated.
Posted on August 26, 2015
| Category | Primary
data source | Primary
identifier |
| Eukaryotes | RefSeq | GeneID |
| Prokaryotes (reference) | RefSeq | Locus_tag |
| Prokaryotes (the rest) | GenBank | Locus_tag |
| Viruses (vg) | RefSeq | GeneID |
| Plasmids (pg) | RefSeq | GeneID |
| Addendum (ag) | PubMed | ProteinID |
Transition from SOAP to REST
In the KEGG release 63.0 on July 1, 2012 a new version of the KEGG API was made available. It is a REST-based API service, replacing the previous SOAP-based API service.
The new service contains most of the capabilities of the previous service, and provides additional features for systematically handling KEGG identifiers. For example,
/list/hsa
will list the entire set of human genes,
/conv/ncbi-gi/hsa
will convert the entire set of KEGG human gene identifiers to NCBI gi numbers (and vice versa), and
/link/pathway/hsa
will identify KEGG pathway maps that contain each of the human genes. It is also possible to limit the gene set by changing "hsa" to "hsa:10" for a single gene, "hsa:10+hsa:100" for two genes, etc.
The previous SOAP-based API service has not been updated for five years (see
ChangeLog) and has become obsolete in certain aspects. Because the original developer is no longer with us at KEGG, we have decided to move to the new service with a much simpler design. The old service will continue to be accessible for six months, until December 31, 2012.
Posted on June 4, 2012
Revised on July 1, 2012
Announcement: Four-letter organism codes
To accommodate the rapid increase of new genomes, the KEGG organism code is no longer limited to three letters. The current KEGG relational database schema allows up to five letters, but for now we will be using either a three- or four-letter code for an organism in the GENES (high-quality complete genome) category. Note that the four letter codes starting with "d" for DGENES and starting with "e" for EGENES had been abolished. Organisms in these categories are identified by the T numbers only.
Posted on June 4, 2012
Revised on July 1, 2012
Important Announcement: 50th Release of KEGG
KEGG will soon be making its 50th release.
We would like to take this opportunity to thank you for your ongoing support and to announce an important milestone in the evolution of the KEGG project.
For almost a year we have been gradually upgrading the internal system for the development and maintenance of the KEGG database. The introduction of a new genome annotation procedure is already in place as of January 1, 2009 (see the
KO page). We are now preparing for a most significant change involving KEGG pathway maps, which will be introduced as part of the next scheduled release on April 1, 2009. All pathway maps are being redrawn using a newly developed tool called KegSketch, which generates SVG and KGML files. Internally the pathway map update/coloring procedure will be based on the text manipulation of SVG files rather than the color manipulation of GIF files. For outside services we will continue to provide facilities to color pathway map image files, but there are some differences:
- The map image files will be changed from GIF to PNG in order to accommodate more colors. This will happen between May and July.
- Starting in April only the GIF (or PNG) and html files of each pathway map will be provided at the ftp site. Auxiliary files such as conf and coord will have to be created, if necessary, from the html file by the user.
Because GIF is limited to 256 colors, we have been experiencing problems to properly manipulate KegSketch generated pathway maps that are already in use. The quality of embedded illustrations deteriorated because we have not redrawn them yet and have simply incorporated them as unedited images. We expect that these and other problems will be resolved once our new system is fully operational by the summer of this year.
The KEGG project is now 14 years old and the transition to the new system is necessary for the long-term stability of the project. Thank you for your continued support of KEGG.
Minoru Kanehisa
KEGG Project Leader
First posted on February 5, 2009
More details added on February 16, 2009