Database Resources
GlyCosmos
A Web portal for glycoscience data based on Semantic Web technology. Glycan-related data including genes, proteins, lipids, pathways, diseases and organisms can be cross-searched, and all entries are linked with other data where available.
| Data in Database | glycan structures, proteins, genes, lipids, pathways, diseases, organisms, etc. |
| Search Options | glycan search options: substructure, subsumption, composition; text search across all data |
| Availability | https://glycosmos.org |
| License | CC-BY-4.0 |
| Status | stable, maintained |
| Funding | JST/NDBC of Japan |
| Future Plans | - |
| Code Availablity | on request; Data Download and SPARQL endpoints available |
| Contact | Kiyoko F. Aoki-Kinoshita: kkiyoko@soka.ac.jp |
GlyGen
GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. The GlyGen web portal allows exploration of this data and execution of unique searches that cannot be performed using any of the integrated databases in isolation. GlyGen also provides machine readable APIs and a SPARQL endpoint to access the integrated data.
| Data in Database | glycan structures, proteins, genes, enzymes, diseases, organisms, papers etc. |
| Search Options | glycan search options: identifier, mass, classification, subsumption, composition etc.; protein search options: identifiers, attached glycans, GO terms, PTM, disease etc.; combined search options using protein and glycan search criteria |
| Availability | https://www.glygen.org |
| License | CC-BY-4.0 |
| Status | stable, maintained |
| Funding | NIH Glycoscience Common Fund |
| Future Plans | Adding more species to the database; Adding lipids to the database; Structure based search options |
| Code Availablity | GitHub |
| Contact | GlyGen Consortium myglygen@gmail.com |
GlyTouCan
The international glycan repository where users can register structures and obtain an accession number once validated. Glycan database developers can become “GlyTouCan Partners” to link their data with GlyTouCan automatically. More advanced search functionality is available from GlyCosmos at https://glycosmos.org.
| Data in Database | structure, databases references, species annotation |
| Search Options | sub-structure search |
| Availability | https://glytoucan.org |
| License | CC-BY-0 |
| Status | stable, maintained |
| Funding | JST/NDBC of Japan |
| Future Plans | - |
| Code Availablity | on request |
| Contact | Kiyoko F. Aoki-Kinoshita: kkiyoko@soka.ac.jp |
GlycomeDB
Meta database that integrates the structures from several glycomics databases (CFG, KEGG, GLYCOSCIENCES.de, GlycoBase, JCGGDB, BCSDB, PDB, GlycO and Carbbank) into one consistent sequence representation and creating a unique index of all structures present in the integrated database. Species annotations from the other databases are retrieved as well and integrated using the NCBI Taxonomy. Each structure in GlycomeDB is linked back to the original database allowing finding and browsing all occurrences of a structure in multiple databases.
| Data in Database | structure, databases references, species annotation |
| Search Options | structure search, sub-structure search, similarity search, maximum common substructure search, species search |
| Availability | http://www.glycome-db.org |
| License | None |
| Status | stable, maintained |
| Funding | - |
| Future Plans | - |
| Code Availablity | on request |
| Contact | Rene Ranzinger: rene@ccrc.uga.edu |
UniCarbKB
The UniCarb KnowledgeBase (UniCarbKB) offers public access to a growing, curated database of information on the glycan structures of glycoproteins. UniCarbKB is an international effort that aims to further our understanding of structures, pathways and networks involved in glycosylation and glyco-mediated processes by integrating structural, experimental and functional glycoscience information. This initiative builds upon the success of the glycan structure database GlycoSuiteDB, together with the informatic standards introduced by EUROCarbDB, to provide a high-quality and updated resource to support glycomics and glycoproteomics research. UniCarbKB provides comprehensive information concerning glycan structures, and published glycoprotein information including global and site-specific attachment information.
| Data in Database | structure, glycoproteins, site-specific information, databases references, species annotation, tissue, cell line, biological fluid, methods |
| Search Options | structure search, sub-structure search, species search, glycoprotein search, UniProtKB accession number search, tissue search, composition search |
| Availability | http://unicarbkb.org |
| License | CC |
| Status | stable, maintained |
| Funding | The National eResearch Collaboration Tools and Resources (NeCTAR) Project; Swiss National Science Foundation |
| Future Plans | Continued curation, better integration and support for GlycoRDF, improved search and query functionality |
| Code Availablity | Release 1 GitHub public, On-going developments BitBucket user managed |
| Contact | - |
Carbohydrate Structure Database (CSDB)
The Carbohydrate Structure Database (CSDB) stores structural, bibliographic, taxonomic, NMR spectroscopic, and other data on natural carbohydrates and their derivatives published in the scientific literature. The CSDB project was launched in 2005 for bacterial saccharides (as BCSDB). The database focuses mainly on glycans, glycopolymers, and glycoconjugates of microorganisms. It provides close-to-complete coverage on prokaryotes, fungi, and protista, and partial (up to 2001) coverage on plants. CSDB is regularly updated via manual expert annotation of original publications. Both newly annotated data and data imported from other databases are manually curated. The CSDB data are exportable in many formats, including GlycoRDF. CSDB providesserves as platform for glycoinformatic services. They include SNFG-compatible graphic structure editor with live update of multiple notations and simulated atomic coordinates, accurate simulation of 1H, 13C and 2D NMR spectra of saccharides, NMR-based structure prediction, glycome-based taxon clustering, prediction of molecular geometry of oligosaccharides, and other. The CSDB portal hosts additional databases for glycosyltransferases with confirmed activity, glycan conformation maps, aglycons, monomers, glycoepitopes, etc.
| Data in Database | structures, assigned NMR spectra, taxon annotations, bibliographic annatations, databases references, conformations, GT activity, supplementary data |
| Search Options | structure search, sub-structure search, composition search, taxon search, bibliography search, NMR signal search, id search |
| Availability | http://csdb.glycoscience.ru |
| License | None (free) |
| Status | stable, maintained, updated annually |
| Coverage | aims to be complete for glycans of bacteria, archaea, protista, fungi up to now; for plants up to 2001. Current coverage overview: http://csdb.glycoscience.ru/database/core/covstats.html |
| Curated | yes |
| Funding | Russian Foundation for Basic Research, Russian Science Foundation, Deutches Krebbsforschungszentrum |
| Future Plans | see papers (http://csdb.glycoscience.ru/help/credits.html#refs) |
| Data Availablity | RDF feed, flat dumps, SQL (see DOI 10.1038/s41597-022-01186-9) |
| Code Availablity | no |
| Contact | Phyl Toukach: netbox@toukach.ru |
SugarBindDB
The SugarBind Database (SugarBindDB) covers knowledge of glycan binding of human pathogen lectins and adhesins. It is a curated database; each glycan-binding event is associated with at least one published reference. The core data of SugarBindDB is a triple constituted of a pathogenic agent, a lectin/adhesin and a glycan ligand. SugarBindDB content is displayed in views. All views are interconnected.
| Data in Database | structure, pathogenic lectin/adhesin, protein-carbohydrate interactions, cross-references, binding annotation, tissue, disease, symptoms, methods |
| Search Options | species search, lectin search, ligand search, tissue search, disease search, multi-criteria search |
| Availability | http://sugarbind.expasy.org |
| License | CC |
| Status | stable, maintained |
| Funding | SIB Swiss Institute of Bioinformatics + Swiss National Fund |
| Future Plans | increased data integration, continued data curation, addition of binding prediction tools |
| Code Availablity | https://bitbucket.org/sib-pig/sugarbind |
| Contact | - |
Glycosciences.DB
Database of the Glycosciences.de portal. Contains CarbBank structures + PDB carbohydrates + structures with NMR shifts extracted from the literature.
| Data in Database | structure, 3D structure models, pdb data, nmr shifts, species annotation, literature references |
| Search Options | structure search, sub-structure search, motif search, n-glycan properties search, literature search, nmr peak search |
| Availability | http://www.glycosciences.de/database |
| License | None |
| Status | stable, maintained |
| Funding | - |
| Future Plans | - |
| Code Availablity | - |
| Contact | Thomas Lütteke: thomas.luetteke@vetmed.uni-giessen.de |
MonosaccharideDB
Monosaccharide database. Contains monosaccharides + name parsing / encoding routines.
| Data in Database | monosaccharide properties, residue names |
| Search Options | name search, properties search |
| Availability | http://www.mononsaccharidedb.org |
| License | - |
| Status | stable, maintained |
| Funding | - |
| Future Plans | - |
| Code Availablity | - |
| Contact | Thomas Lütteke: thomas.luetteke@vetmed.uni-giessen.de |
GlycoMapsDB
Database of conformational maps of glycosidic linkages
| Data in Database | conformational maps derived from MD simulations |
| Search Options | disaccharide search |
| Availability | http://www.glycosciences.de/modeling/glycomapsdb |
| License | - |
| Status | stable |
| Funding | - |
| Future Plans | - |
| Code Availablity | - |
| Contact | Thomas Lütteke: thomas.luetteke@vetmed.uni-giessen.de |
GlycoPattern
GlycoPattern is currently in the process of identifying new funding for hosting. It is a web-based bioinformatics resource to support the analysis of glycan array data for the Consortium for Functional Glycomics. This resource includes algorithms and tools to discover structural motifs, a heatmap visualization to compare multiple experiments, hierarchical clustering of Glycan Binding Proteins with respect to their binding motifs and a structural search feature on the experimental data.
| Data in Database | - |
| Search Options | - |
| Availability | https://glycopattern.emory.edu |
| License | - |
| Status | - |
| Funding | - |
| Future Plans | - |
| Code Availablity | - |
| Contact | sanjay.agravat@emory.edu |
UniCarb-DB
UniCarb-DB is the glycomics fragmentation database that stores, integrates and processes data from manually annotated ms spectra.
| Data in Database | MS/MS spectra, structures, peak lists, references, methods, tissue and taxonomy annotations |
| Search Options | Species, tissue, composition, recorded mass, observed mass, peak list |
| Availability | http://www.unicarb-db.org |
| License | CC |
| Status | Stable, maintained |
| Funding | NeCTAR, ANDS, STINT, SIB ExPASy |
| Future Plans | - |
| Code Availablity | Open Source |
| Contact | niclas.karlsson@medkem.gu.se |
GlycoNAVI
GlycoNAVI is the Carbohydrate database to support carbohydrate research. Contains glycan structures, chemical synthesis, anomeric isomer proportion, NMR spectra, activity, 3D-structures, and carbohydrate-protein interaction extracted from literatures.
| Data in Database | Glycan structures, chemical synthesis, carbohydrate-protein interaction, 3D-structures, and linked to other related databases. |
| Search Options | |
| Availability | https://glyconavi.org |
| License | CC-BY |
| Status | stable, maintained |
| Funding | Integrated Database Project of Japan, KAKENHI |
| Future Plans | |
| Code Availablity | |
| Contact | Issaku Yamada: yamadaissaku@gmail.com |