GlyCosmos Portal

Submissions

Overview

The GlyCosmos Portal is a Web portal aiming to integrate the glycosciences with the life sciences.
It consists of Standards, Repositories and Data Resources, providing information about genes, proteins, lipids, pathways and diseases.
GlyCosmos has been recognized as the official portal of the Japanese Society for Carbohydrate Research.

Standards

WURCS

A text representation for glycan structures aimed for use in the Semantic Web.

GlycoRDF

A standard ontology for RDFizing glycomics data (glycan structures, publications, experimental data, and source).

GlycoCoO

A standard ontology for RDFizing glycoconjugate data (glycoproteins/glycolipids, glycan abundance ratios, sample information, diseases, publication information, etc.)

Repositories

GlyTouCan

The glycan structure repository GlyTouCan assigning accession numbers to glycans.

GlyComb

GlyComb is a repository for glycoconjugate information, including glycopeptides, glycoproteins, glycolipids and glycosides. At the current prototype stage, GlyComb takes as input glycopeptides and the glycans attached to them (specified as GlyTouCan IDs).

GlycoPOST

The glyco(proteo)mics repository GlycoPOST stores mass spectrometry data obtained from glyco(proteo)mics related experiments.

UniCarb-DR

UniCarb-DR was launched in 2019 in order to provide a forum for depositing annotated glycomic MS/MS spectra according to the MIRAGE reporting guidelines for glycomic experiments. UniCarb-DR allows data to be uploaded as part of scientific publications, fulfilling the requirement for data open access.

Data Resources and Tools

All data in GlyCosmos are stored using Semantic Web technologies, enabling easier integration with life science data.

Genes 393515 Entries

Integrated list of glycan-related genes extracted KEGG GENES Database, UniProt, GlycoGene Database (GGDB), Plant GARDEN and FlyGlycoDB. Glycan-related genes including glycosyltransferase, hydrolase activity (acting on glycosyl bonds), carbohydrate metabolic process, etc .

Glycoproteins 126547 Entries

Integrated list of glycoproteins extracted from UniProt and annotated with glycosylation data from GlyGen, GlyConnect, GlycoProtDB and The O-GlcNAc Database. For each entry, information such as glycosylation site, glycans, diseases, 3D structures, and pathway information are available.

Lectins 5271 Entries

Integrated list of Lectins, including proteins with carbohydrate binding function obtained from UniProt and lectin data from Lectin Frontier DataBase (LfDB), UniLectin and CarboGrove. Glycosylation site information, along with glycan-binding patterns are also integrated where available.

Glycolipids 6046 Entries

Glycolipid entries from the LIPID MAPS Structure Database (LMSD).

Glycans 244842 Entries

The list of validated glycans extracted from GlyTouCan, updated weekly.

Pathways 8115 Entries

Integrated of pathway data, containing glycoproteins and glycans obtained from Reactome and the Metabolism of carbohydrates in Escherichia coli O-antigens obtained from ECODAB. Search by pathway name, species, and protein name.

Diseases 7942 Entries

List of diseases involving glycan related genes. The information of each database of Glyco-Disease Genes Database (GDGDB), DisGeNET, and Alliance of Genome Resources is integrated into one list.

Organisms 30690 Entries

List of all species in GlyCosmos Resources.

Cross Search Release Statistics Download

SugarDrawer

SugarDrawer is a simple user interface providing the basic functionality for drawing and searching glycan structures with known topology. Those who wish to draw more complex glycans can use the Web version of GlycanBuilder.

GlycanBuilder

Web-based user interface for GlycanBuilder, with all the functionality provided by the standalone version. Databases including GlyTouCan, GlyCosmos glycans and GlycoNAVI can also be searched.

Glycan Converters

Glycan structure conversion tools between WURCS, GlycoCT, IUPAC, etc. Image generation and validation functionality are also available.

GlycoMaple

GlycoMaple is a visualization tool for glycosylation pathways in human and mouse. Glycogene expression data can be uploaded or selected from RNA-Seq data from the Human Protein Atlas in the mouse version. Similar data can be selected from Mouse Haemopedia for cell lines in mouse. The expression values will be reflected across various glycan-related pathways at once, and comparisons can be made between samples.

GlycomeAtlas

GlycomeAtlas is a specialised database that provides comprehensive information on glycan structures and their distribution in different human, mouse and zebrafish t

LM-GlycomeAtlas

LM-GlycomeAtlas is a web tool visualizing the data from Lectin Array analyses by the Kuno Laboratory at AIST.

GALAXY

GALAXY (Glycoanalysis by the Three Axes of MS and Chromatography) is a database of elution data on glycan structures of glycoproteins analysed by high-performance liquid chromatography (HPLC). The database includes data on 650 neutral, sialylated, glucuronylated, and/or sulfated N-linked oligosaccharides, which are expressed by a diagram in the shape of a tree with a tri-mannosyl core as the trunk and spreading branches .

MCAW

Glycan structure alignment tool for multiple glycan structures to analyze their commonalities as glycan profiles.

GlycoSim

Glycan biosynthesis simulation tool.

GRable

GRable is a software to estimate site-specific glycan compositions of glycopeptides, using an MS1-based glycoproteomic method named “Glyco-RIDGE” [Narimatsu et al. JPR2018].

Programmatic Access

Members

Japanese Society of Carbohydrate Research Glycoscience Portal GlyCosmos Steering Committee

Name	Affiliation	Position
Kiyoko F. Aoki-Kinoshita	Soka University	Professor (Committee Chair)
Osamu Kanie	Tokai University	Professor
Toshisuke Kawasaki	Ritsumeikan University	Senior Researcher
Tadashi Suzuki	RIKEN	Chief Scientist
Kiichiro Totani	Seikei University	Professor
Naoki Itano	Kyoto Sangyo University	Professor
Shunji Natsuka	Niigata University	Professor
Shoko Nishihara	Soka University	Professor
Yoshiki Yamaguchi	Tohoku Medical and Pharmaceutical University	Professor
Chihiro Sato	Nagoya University	Professor
Koichi Kato	National Institutes of Natural Sciences	Professor
Issaku Yamada	The Noguchi Institute	Chief Scientist (Deputy Chair)

Contributors

Soka University

Kiyoko F. Aoki-Kinoshita
Masaaki Shiota
Tamiko Ono
Sunmyoung Lee
Thukaa Kuoka
Sachiko Akase
Haruko Kitakaze
Isami Sogabe
Kotarou Hayashi
Takafumi Ogura
Hiromi Nagamatsu
Sakura Kiyama
Atsushi Wakamatsu
Nozomi Hatanaka
Miyuki Kikuchi
Eijiro Amagasa
Ran Fukazawa(Intern)
Ryuho Kumashiro

The Noguchi Institute

Issaku Yamada
Shinichiro Tsuchiya
Masaaki Matsubara
Nobuaki Miura
Aiko Hiraki
Naoki Kimura

Nagoya University

Akihiro Fujita

DBCLS

Masae Hosoda

Niigata University

Shujiro Okuda
Yu Watanabe
Akira Seno

AIST

Kiyohiko Angata
Noriaki Fujita
Yoshinori Suzuki
Chiaki Nagai-Okatani
Atsushi Kuno
Hiroyuki Kaji
Hisashi Narimatsu

SparqLite LLC.

Nobuyuki P. Aoki
Daisuke Shinmachi