The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (KEGG GENES) and the chemical space (KEGG LIGAND), and wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally added to the KEGG suite of databases. This reflects our attempt to computerize functional interpretations as part of the pathway reconstruction process based on the hierarchically structured knowledge about the genomic, chemical and network spaces. In accordance with the new chemical genomics initiatives, the scope of KEGG LIGAND has been significantly expanded to cover both endogenous and exogenous molecules. Specifically, RPAIR contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions, such as the prediction of new reactions and new enzyme genes that would degrade new environmental compounds. Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps.

Glycans are among the most complex biological molecules found in nature, being composed of monosaccharide units in various combinations and linkages, and featuring diverse and asymmetric types of branching. Until the 1970s, glycan structures were generally represented in scientific publications as chemically accurate drawings, or using standard IUPAC-approved abbreviations (Sharon 1986; McNaught 1997; Chester 1998). However, given the complexity of many glycan structures, it became difficult to represent such molecules in publication figures, especially those involving multistep biosynthetic pathways or multiple structures. Thus, various investigators began to use symbols to represent monosaccharides in glycans. In 1978, Kornfeld and colleagues put forward an elegant and simple system for representation of vertebrate glycans (Kornfeld et al. 1978), and it entered into popular use over the next two decades. This system was eventually adopted and standardized by the editors of the first edition of the textbook Essentials of Glycobiology (Varki et al. 1999). While this adoption increased the popularity of the symbols, the system had some limitations and inconsistencies and did not take advantage of color. Anticipating a revision, the editors developed an updated symbol nomenclature, which was made available to the community in 2005 before the publication of the Second Edition (Varki, Cummings, Esko, Freeze, Stanley, Bertozzi, et al. 2009). This nomenclature was adopted and widely disseminated, especially by the NIGMS-funded Consortium for Functional Glycomics (CFG), which also consulted the scientific community on this issue, thus enhancing acceptance. The official version of the Second Edition nomenclature has since been available in the online version of the textbook. A suggested extended version was then presented at the website Glycopedia. Meanwhile, alternate symbol nomenclature systems have been proposed (Harvey et al. 2009). Issues regarding nomenclature tend to be more controversial than the underlying science (Varki, Cummings, Esko, Freeze, Stanley, Marth, et al. 2009), as there is never one correct answer, and some aspects are matters of taste. For example, the two systems mentioned each have some relative advantages and disadvantages.

The Symbol Nomenclature for Glycans (SNFG) is a community-curated standard for the depiction of monosaccharides and complex glycans using various colored-coded, geometric shapes, along with defined text additions. It is hosted by the National Center for Biotechnology Information (NCBI) at the NCBI-Glycans Page (www.ncbi.nlm.nih.gov/glycans/snfg.html). Several changes have been made to the SNFG page in the past year to update the rules for depicting glycans using the SNFG, to include more examples of use, particularly for non-mammalian organisms, and to provide guidelines for the depiction of ambiguous glycan structures. This Glycoforum article summarizes these recent changes.

Bioinformatics approaches to carbohydrate research have recently begun using large amounts of protein and carbohydrate data. In this field called glycome informatics, the foremost necessity is a comprehensive resource for genome-scale bioinformatics analysis of glycan data. Although the accumulation of experimental data may be useful as a reference of biological and biochemical information on carbohydrates, this is insufficient for bioinformatics analysis. Thus, we have developed a glycome informatics resource (http://www.genome.jp/kegg/glycan/) in KEGG (Kyoto Encyclopedia of Genes and Genomes), an integrated knowledge base of protein networks, genomic information, and chemical information. This review describes three noteworthy features: (1) GLYCAN, a database of carbohydrate structures; (2) glycan-related pathways; and (3) Composite Structure Map (CSM), a map illustrating all possible variations of carbohydrate structures within organisms. GLYCAN includes two useful tools: an intuitive drawing tool called KegDraw, and an efficient glycan search and alignment tool called KEGG Carbohydrate Matcher (KCaM). KEGG’s glycan biosynthesis and metabolism pathways, integrating carbohydrate structures, proteins, and reactions, are also a pivotal resource. CSM is constructed as a bridge between carbohydrate functions and structures. CSM is able to display, for example, expression data of glycosyltransferases in a compact manner. In all the KEGG resources, various objects including KEGG pathways, chemical compounds, as well as carbohydrate structures are commonly represented as graphs, which are widely studied and utilized in the computer science field.

For the reproducibility and sustainability of scientific research, FAIRness (Findable, Accessible, Interoperable and Re-usable), with respect to the release of raw data obtained by researchers, is one of the most important principles underpinning the future of open science. In genomics and transcriptomics, the sharing of raw data from next-generation sequencers is made possible through public repositories. In addition, in proteomics, the deposition of raw data from mass spectrometry (MS) experiments into repositories is becoming standardized. However, a standard repository for such MS data had not yet been established in glycomics. With the increasing number of glycomics MS data, therefore, we have developed GlycoPOST (https://glycopost.glycosmos.org/), a repository for raw MS data generated from glycomics experiments. In just the first year since the release of GlycoPOST, 73 projects have already been registered by researchers around the world, and the number of registered projects is continuously growing, making a significant contribution to the future FAIRness of the glycomics field. GlycoPOST is a free resource to the community and accepts (and will continue to accept in the future) raw data regardless of vendor-specific formats.