Major changes in the GenomeNet WWW server

• KEGG release 42.0 features:
  (1) a new version of the hierarchical text file viewer such as this.
  (2) sequence information added to PK/NRP entries in the COMPOUND database such as this,
  (3) EXPRESSION database linked to KegArray, and
  (4) new directory organization of the KEGG FTP site.

• In the DBGET system, the database name KO is now treated as abbreviation of the KEGG ORTHOLOGY database.

• The KEGG KEGG top page is modified in release 41.1, introducing a new search box.
• New software GENIES is released for prediction of gene networks by integrating heterogeneous data sets.
• The current web browser-based service of the KEGG EXPRESSION database will end on March 31, 2007.

• In KEGG release 41.0, a new interface is introduced to search all BRITE hierarchies.

• In KEGG release 40.0,
  (1) the BRITE database collection is expanded both for hierarchical text files and binary relation files,
  (2) an updated version of the RPAIR database is released, and
  (3) KEGG documentation pages are reorganized including the new page for KEGG identifiers.

• KEGG release 39.0 includes, for the first time, a Japanese language interface to the KEGG system.
• KEGG update notes are now available in RSS feeds.

• As an extension of the KEGG pathway mapping, the mapping to BRITE hierarchies is implemented. It is an operation to combine two files: a binary relation file and a hierarchical text file.
• Links to the ortholog group tables have been deleted in the pathway menu page, although the tables are still available (for the time being) from the links in the individual pathway maps.
• The essence of the ortholog group tables is being incorporated into the new collection of KEGG pathway modules.
• Additionally, in KEGG release 38.1, KEGG SSDB is separated from KEGG GENES.

• In KEGG release 38.0, KEGG BRITE has been significantly enhanced;
  (1) it is now part of the DBGET system as a collection of hierarchical text files,
  (2) triangles are used to expand/collapse branches in the hierarchical text browser like this, and
  (3) BRITE files can also be viewed by the new desktop application KegHier.
  KegHier has features to handle tab-delimited fields, to create the user's own file list, to integrate personal files with KEGG and other internet resources, and to use Japanese language.
• EGassembler for automatic generation of EST consensus contigs is officially released.

• In KEGG release 37.0, 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, consisting of KEGG DRUG structure maps is released in KEGG release 36.1.
• Manually drawn glycan structures are included in the KEGG PATHWAY database to supplement computationally generated Composite Structure Map (CSM).

• KEGG release 36.0 includes:
  (1) preliminary release of KEGG DRUG for drug information, and
  (2) update of KEGG REACTION with the RPAIR database now containing structural transformation (RDM) patterns.

• KEGG release 35.1 is a minor revision of its top page.

• A new version of KegDraw is released with an enhanced user interface and the PubChem structure search.

• In KEGG release 35.0, BRITE is enhanced with:
  (1) KEGG automatic annotation server, named KAAS, to assist annotation (KO assignment) and KEGG pathway mapping of newly determined genomes, and
  (2) cross-reference lists between KEGG and outside databases.

• KEGG API 4.0 is released providing, among others, methods for KEGG LIGAND.

• KegDraw for drowing chemical compound and glycan structures is released.

• A new interface for glycome informatics, KEGG GLYCAN, is introduced.
• The server-side redirection from ".genome.ad.jp" to ".genome.jp" is terminated for blast, fasta, motif, and clustalw services.

• A renewal is given to the entire GenomeNet pages.
• KEGG release 34.0 contains the following features:
  (1) new interfaces to the KEGG system in the KEGG2 (table of contents) page,
  (2) organism-specific views of KEGG, such as for human and E. coli,
  (3) KEGG pathways linked to many different outside databases, such as NCBI Entrez and UniProt,
  (3) customization of KEGG organism menu (Cookie must be enabled in your browser),
  (4) automatic annotation and pathway mapping of draft genomes (DGENES) and EST consensus contigs (EGENES), which significantly increased the number of KEGG Organisms,
  (5) KEGG BRITE officially introduced as the fourth component of KEGG, and
  (6) new BRITE features including classifications of drugs and compounds.
• New interfaces are introduced to DBGET and LinkDB searches.
• New interfaces are introduced to BLAST and FASTA searches.
• New multiple alignment programs MAFFT and PRRN are available in addition to CLUSTALW.

• New features of KEGG release 33.0:
  (1) a glycomics resource KEGG GLYCAN Composite Structure Map for examining organism-specific glycan structures,
  (2) first examples of the high-level KEGG pathway map (overview of biosynthetic pathways) and the classification of compounds (therapeutic category of drugs),
  (3) a preliminary version of the EGENES database, a collection of EST contigs computationally generated from massive EST data for various plants.

• An updated version of KegArray for microarray data analysis is released for both Mac OS X and Windows XP.

• KEGG release 32.0 is a major update for the LIGAND database containing:
  (1) the Oracle version of LIGAND replacing the ISIS version,
  (2) new programs SIMCOMP and SUBCOMP for database searching of similar compound structures,
  (3) an updated version of KCaM for database searching of similar glycan structures,
  (4) a new program e-zyme to predict reactions between given compound pairs with assignments of possible EC numbers, and
  (5) the new database named RPAIR for the reactant pairs that constitute enzymatic reactions with information about atomic alignments.

• A new download page is introduced.

• A new KO page is introduced.

• The performance of the gene cluster search program in the KEGG SSDB database has been improved dramatically. By clicking on the "Gene cluster" button on a GENES entry such as this, conserved gene clusters (sets of orthologous genes that are adjacent on the chromosome) are displayed either in a tabular form, which is similar to the KEGG ortholog group table, or in a graphical form, which is suitable for distinguishing gene functional categories by the coloring.

• The Web addresses in the older form of "genome.ad.jp" are automatically redirected to "genome.jp".

• A new version of the bget program is now used to display DBGET entries of all components of the KEGG GENES database (GENES, GENOME, and KO) and the KEGG LIGAND database (COMPOUND, GLYCAN, REACTION, and ENZYME), together with brief help files.

• A new metablic pathway category, "Biosynthesis of Polyketides and Nonribosomal Peptides", is added to the hierarchy of the KEGG pathways and the KO.

• New features of KEGG release 31.0:
  (1) A new display format is being introduced to the DBGET entries of the KEGG databases, starting with the GENES database such as this.
  (2) The interface for the GENES database is updated.
  (3) The separate interface for the SSDB database is re-installed.

• The hierarchy of the KEGG pathways and the KO has been slightly modified, "Glycan Biosynthesis and Metabolism" replacing "Metabolism of Complex Carbohydrates" and "Metabolism of Complex Lipids".

• The COMPOUND and GLYCAN entries now contain the KCF (KEGG Chemical Function) representation of the 2D coordinates and connection patterns. They are indicated in the ATOM/BOND lines and NODE/EDGE lines, respectively, in COMPOUND and GLYCAN.

• New features of KEGG release 30.0:
  (1) KGML (KEGG Markup Language) is updated to version 0.4.
  (2) A preliminary version of KegArray, a Java application for microarray data analysis, is released for Mac OS X.
  (3) In response to popular demands, the KEGG pathways are linked again to human diseases genes in the OMIM database, such as like this.
• The TRANSFAC database is no longer supported in GenomeNet because updated versions are not made publicly available.

• KEGG release 29.0 contains the following new features:
  (1) new user interfaces including PATHWAY for both metabolic and regulatory pathways, GENES for GENES, GENOME, and SSDB queries, and LIGAND for the new LIGAND home page,
  (2) a new version of the KEGG genome map browser without using Java applet, and
  (3) an improvement (coloring of gene clusters) in the automatic generation of ortholog group tables.

• The XML version (KGML v0.3) of KEGG regulatory pathways is now available in KEGG 28.0.

• The GLYCAN database is released in KEGG 27.0 as a new effort to collect complex carbohydrate structures, some of which are linked to/from KEGG pathways such as this. The database size will grow rapidly for a while, since unique structures are being extracted from CarbBank. Both GLYCAN and CarbBank are now part of the DBGET system, and substructure searches can be made thourgh a Java-based interface. Try clicking on the structure image in an GLYCAN entry such as this.

• The TrEMBL and TrEMBL_new databases have been installed in the DBGET system, and also in the BLAST and FASTA searches.

• A new service, KEGG API, is available in KEGG release 26.0. It is a SOAP interface suitable for automating access to and use of KEGG.
• Other features in KEGG release 26.0 include:
  (1) KGML (KEGG Markup Language) version 0.2,
  (2) a new query interface for the SSDB database,
  (3) a new top page for the EXPRESSION database, and
  (4) a new popup menu to limit the number of organisms shown in the KEGG Table of Contents page.

• KEGG release 25.0 is a major update containing:
  (1) the first release of KEGG pathways in XML together with the specification of KGML (KEGG Markup Language),
  (2) the official release of KO (KEGG Orthology), which consists of entries such as this,
  (3) links from KO to other resources, especially the results of computational clustering of the SSDB database such as this,
  (4) implementation of KO database as part of the DBGET system,
  (5) 'all organisms' pathways linked to KO such as this, and
  (6) new reference metabolic pathways linked to reaction data such as this.

• A new version of AAindex is released with application programs and data submission form.
• In KEGG release 24.0 the GENES and SSDB databases are operational on Oracle. SSDB now contains TIGRFAMs in addition to Pfam and Prosite.

• KEGG release 23.0 comes with the DBGET search capability for the REACTION database.

• A new version of LinkDB is released, allowing searches against the web of molecular biology databases for entries that are related to single, multiple, or all entries in a given database. The database versus database search capability is especially useful, for example, for mapping genes of a given organism against KEGG pathways.

• New databases are released in the Genome Databses in Japan. One is a completely updated version of BSORF for the Bacillus subtilis genome and the other is SYORF for community annotaion of cyanobacterial genes.

• New features of KEGG release 22.0:
  (1) The top category of "Human Diseases" is introduced in the hierarchy of KEGG pathways, as shown in the regulatory pathways section.
  (2) The top category of "Cellular Processes" is also being reorganized.
  (3) The hierarchy of KEGG pathways is now called KO (KEGG Orthology). The KO identifiers will be introduced shortly.
• A new version of DBGET links diagram is available.

• Starting in KEGG release 21.0, an emphasis of data collection efforts will be placed more on eukaryotic species.
• In order to cope with an increasing number of bacterial and archaeal species, the ortholog group tables will be maintaned only for representative sets of organisms. Each table now contains a "select organism" link to computationally add or delete selected organisms.

• The new LIGAND database is released as KEGG release 20.1. It is a Chemscape version enabling substructure searches against COMPOUND and REACTION by installing Chime and ISIS/Draw.

• The KEGG ftp site (ftp://kegg.genome.ad.jp/) is no longer available; it is limited to the users with proper license agreements. All the KEGG data including LIGAND may be obtained from the GenomeNet ftp site (ftp://ftp.genome.ad.jp/pub/kegg/), as long as they are used by academic users for academic purposes.

• The DBGET system now provides full text search for the DNA databases (GenBank and/or EMBL).
• In KEGG release 20.0 the Java-based dendrogram viewer is implemented in both the Expression database and the SSDB database.

• KEGG release 19.0 provides the following features:
  (1) The KEGG Expression Database contains an increasig amount of microarray gene expression profile data for Synechocystis PCC6803 and Bacillus subtilis, together with an enhanced version of KEGG expression browser.
  (2) 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.

• The GenomeNet service is now part of the official activities of the newly established Kyoto University Bioinformatics Center.
• A new database named SSDB is implemented in KEGG release 18.0. 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.

• In KEGG release 17.0 the following features have been made available:
  (1) a hierarchy of organism groups in the KEGG menu page and associated DBGET search, and
  (2) 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.

• KEGG release 16.0 provides enhancements in handling cell lineages and gene expression data:
  (1) The cell lineage of H.roretzi is now represented by a graphical image map, which is linked to actual pictures of early-stage embryo.
  (2) Different types of analysis tools for microarray expression data are being integrated into a single interface of KEGG expression database.

• The gene catalog search in KEGG is incorporated in the DBGET/LinkDB system as the hfind mode, such as for searching Synechocystis.
• In KEGG release 15.0 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 NCBI RefSeq database is implemented in the GenBank portion of the DBGET/LinkDB system.

• KEGG release 14.0 contains the following new features:
  (1) 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.
  (2) As a result of this extension, KEGG metabolic pathways may now be represented by gene names (or ortholog IDs), such as shown in Biphenyl degradation.
• 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.
• A composite database named MotifDic is defined for searching multiple motif libraries by the DBGET/LinkDB system.
• The role of the BRITE database has been redefined. It now contains different types of binary relations, including generalized protein-protein interactions in KEGG and systematic experimental data by yeast two-hybrid systems, as well as sequence similarities, expression similarities, and chromosomal correlations between two genes.

• KEGG release 13.0 contains the following new features:
  (1) Introduction of the GENOMES database for a collection of completely sequenced genomes.
  (2) Enhancements of the expression map browsers including the new expression clustering tool.

• The GenomeNet servers for BLAST, FASTA, and MOTIF have all been upgraded. BLAST is now version 2.0 and MOTIF incorporates Pfam search and other capabilities.
• To supplement the DBGET/LinkDB system, the full text search STAG is made publicly available.

• In KEGG release 12.0 a new type of hierarchical text data is introduced for browsing cell lineage maps.
• MAGEST for Maboya (the ascidian, Halocynthia roretzi) Gene Expression patterns and Sequence Tags is released as part of the Genome Databases in Japan.

• A preliminary version of expression map browser is made available in KEGG release 11.1 for analyzing microarray gene expression data.

• KEGG release 11.0 contains the following new features:
  (1) In addition to the row-wise extraction, the column-wise extraction of gene definitions is implemented in the ortholog group tables.
  (2) 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).
• New BodyMap server is available in the Genome Databases in Japan.
• TSEG for prediction of membrane proteins is available in the Sequence Interpretation Tools.

• Rat Genome Map is released by the Human Genome Center of the University of Tokyo as part of the Genome Databases in Japan.

• A new version of genome map browser has been implemented in KEGG release 10.0. It now integrates both linear and circular chromosomes, and also incorporates plasmids and extra chromosomal elements.

• Mouse Encyclopedia Index is released by the RIKEN Genomic Sciences Center. It is linked from Genome Databases in Japan.

• In KEGG release 9.0 it has become possible to color genome maps and ortholog tables, in addition to pathway maps.

• KEGG release 8.0 contains a new classification of chemical compounds, which is still preliminary but which will be expanded in future releases.
• Another new feature of this release is the capability to mark KEGG pathways by any combination of colors, which should be useful in coloring genes according to the expression profiles obtained by microarray or DNA chip experiments.

• In KEGG release 7.1 the genome map browser has a new interface that runs much faster than the previous version.
• The KEGG mirror server package (KEGG release 7.1 + DBGET/LinkDB version 1.9) has been release at the KEGG anonymous FTP site. The DBGET/LinkDB system (version 1.9) is also available at the GenomeNet anonymous FTP site.

• KEGG release 7.0 has a new capability to compare two genome maps by a 'dot matrix' of similar genes. This 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.

• KEGG release 6.1:
  (1) A new category of ortholog/paralog group tables is added to the KEGG pathway section.
  (2) 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.
  (3) Started providing a suite of genome map comparison tools, including the search for homologous gene clusters.
• DBGET/LinkDB updates:
  (1) A new interface is implemented for the advanced mode of DBGET search.
  (2) BRITE can now be searched by DBGET.
• A major update release of MOTIF that can be used to:
  (1) Search motif libraries of PROSITE patterns, PROSITE profiles, BLOCKS, ProDom, and PRINTS for proteins, or TRANSFAC for nucleic acids.
  (2) Search sequence databases for a given pattern.
  (3) Generate a user-defined profile from multiple sequence alignment data.

• KEGG release 6.0 contains the following features.
  (1) Genome map search - A new capability to search genome maps for gene positions is released.
  (2) 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.
  (3) In the result of path computation program PathComp, the user can now examine a series of compound structures to select plausible pathways.

• In release 5.0, KEGG starts organizing molecular assemblies as a part of the regulatory pathway section. It also starts organizing different types of molecular catalogs, starting with CD molecules and cytokines in the immune system.

• Pyrococcus horikoshii OT3 database is released by the National Institute of Technology and Evaluation. It is a part of the Genome Databases in Japan.

• HGC has released its Collection of Links Useful for Exploration (CLUE), which is listed in the Links to Molecular Biology Servers in the World.

• In KEGG release 4.1 the compound data has been fully integrated. A circle on the pathway diagram is now a clickable and searchable object.
• The new PATHWAY mail server (pathway@genome.ad.jp) is made available. It performs the KEGG pathway search by EC numbers, compound numbers, and gene names.

• A preliminary version of p53MDB, a p53 mutation database by HGC, is made available in the Genome Databases in Japan.

• KEGG release 4.0 has the following new search capabilities against the KEGG metabolic and regulatory pathways:
  (1) A set of gene names of a given organism can be used as a query to search matching names on the KEGG pathways.
  (2) 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.
  

• The amino acid sequence data in the KEGG gene catalogs (namely, the GENES database) can now be searched by FASTA. It can also be searched either by FASTA or BLAST in the "Sequence Interpretation Tools".

• A new version of TFSEARCH is made available in the "Sequence Interpretation Tools".
• DictycDB by the Japanese Dictyostelium discoideum cDNA Project is now a part of the Genome Databases in Japan.

• KEGG Release 3.1 contains a new collection of regulatory pathways, in addition to the previous collection of metabolic pathways.

• HGC has released MBGD: Microbial Genome Database, which can be accessed from Genome Databases in Japan.

• A new release of the GenomeNet WWW server is made available. There is now the Japanese home page that contains additional materials of the Monbusho Human Genome Program.
• The DBGET/LinkDB system is better integrated and is accessible with the new DBGET links diagram. The KEGG gene catalogs may now be retrieved by DBGET as well.
• The MOTIF server is completely rewritten. It launches RasMol for viewing 3D locations of found motifs. The server also accepts user-defined patterns to be searched against sequence databases.

• The gene finding system GRAIL developed by Oak Ridge National Laboratory is mirrored at HGC under the category of "Sequence Interpretation Tools".

• A new version of LinkDB is released. As shown in the example, there are now three types of links: factual links, sequence similarity links, and biological links. The biological links represent partners for each molecule under biological conditions, which are being computerized in the KEGG project.

• The Release 2.0 of KEGG is made available. The Internet version relies less on Java making it more widely available, while the CD version experiments a number of advanced features of Java and Javascript which may only be appreicated by Netscape 3.01 or later.

• A new distribution policy of KEGG is announced. The weekly updated CD version of KEGG may be downloaded by anonymous FTP.

• The sequence similarity search program FASTA is now available in the "Sequence Interpretation Tools". For the time being the interactive use is limited to protein database searches.

• SOSUI for predicting secondary structures in membrane proteins is now available in the "Sequence Interpretation Tools".

• A new interface named IDEAS was implemented for quick access to DBGET, KEGG, and BLAST.
• The GenomeNet anonymous FTP service has been upgraded.
• The sequence data are made available by the JST large-scale human genome sequencing projects.

• The Java option of KEGG is now fully implemented.

• Human chromosome 21 sequence map by HGC was released.

• The release 1.0 of KEGG is now available.
  This is the first official release of the Internet version of KEGG (Kyoto Encyclopedia of Genes and Genomes), which is our project to make functional catalogs of living organisms and to link them with the gene catalogs obtained by genome sequencing projects. The CD version of KEGG is scheduled to be released in December 1996. Please see the on-line document for details.

• The multiple sequence alignment program CLUSTALW is now available in the "Sequence Interpretation Tools".

• A new interface for the BLAST program has been implemented in the "Sequence Interpretation Tools". The option to submit the query by e-mail has also become available.

• The summary of GenomeNet Database Service is added to the menu of "About the GenomeNet".

• Two helper applications can now be launched from the DBGET system:
  (1) RasMol for the data retrieved from PDB (see example) and
  (2) ISIS/Draw for the data retrieved from LIGAND (see example).
  
• The new release of the LIGAND database consists of the ENZYME and COMPOUND sections.

• The version 2 of DBGET was released. For the users under WWW, the new version includes the following capabilities :
  (1) It is now possible to search DNA or Protein sequence databases as a whole.
  (2) The PATHWAY database under KEGG is integrated in the DBGET system.
  (3) The distinction of bfind and bget modes is made as described in the new document.
  (4) A new DBGET links diagram is available, linking the DBGET and KEGG systems.

• Announcements of genome related events in Japan can be read in English or in Japanese.

• GENOTK Human cDNA Database by Otsuka GEN and HGC was released.

• Database release information may now be viewed from the DBGET links diagram.

• A new version of KEGG was released as described in the release note.

• A major upgrade of the GenomeNet Database Server was relaeased containing two new categories:
  (1) Preliminary release of KEGG (Kyoto Encyclopedia of Genes and Genomes).
  (2) Entry point to Genome Databases in Japan.
  
• BSORF Bacillus subtilis genome database by NIST and HGC was released.
  
• Overview of GenomeNet revised.
  
• Genome Informatics News became on-line.

• TFSEARCH for transcription factor binding site search became available under SIT.
  
• A new tool was developed for handling hierarchical text data, as implemented for Enzyme EC number table.

• Usage Statistics of GenomeNet Database Service may now be viewed on WWW.

• TRANSFAC database became available in DBGET.

• Methods in Computational Molecular Biology became on-line.

• Daily updated GenBank became default GenBank in DBGET.

• HGC User's Guide (in Japanese) became on-line.

• Abstracts and full papers of Genome Informatics Workshops became on-line.

• EPD database became available in DBGET and BLAST.

• BLAST service was initiated under SIT.

• The new category of SIT (Sequence Interpretation Tools) was released.
  MOTIF and PSORT services were initiated under SIT.
  
• Document services were started.

• LINKDB service was started as a part of DBGET. It is now possible to see all available crosslink information for each entry by clicking on the entry name.

• GenomeNet WWW server was announced to world-wide users.

• MEDLINE reference links were included in DBGET.

• The compound section of LIGAND database was implemented in DBGET for viewing of structural formula.

• DBGET implementation was completed and GenomeNet WWW server was experimentally released for domestic HGP researchers.