Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts

Abstract

The Carbohydrate Structure Databases (CSDBs, http://csdb.glycoscience.ru) store 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). Currently, it includes two parts, the Bacterial CSDB and the Plant&Fungal CSDB. In March 2015, these databases were merged to the single CSDB. The combined CSDB includes information on bacterial and archaeal glycans and derivatives (the coverage is close to complete), as well as on plant and fungal glycans and glycoconjugates (almost all structures published up to 1998). 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 a number of modern formats, such as GlycoRDF. CSDB provides additional services for simulation of 1H, 13C and 2D NMR spectra of saccharides, NMR-based structure prediction, glycan-based taxon clustering and other.

Biopolymer Skeleton Produced by Rhizobium radiobacter: Stoichiometric Alternation of Glycosidic and Amidic Bonds in the Lipopolysaccharide O‐Antigen

“…As for Poly2 , it is built up of a disaccharide repeating unit made of l ‐rhamnose and d ‐fucose (Figure ), the latter being the less common fucose stereoisomer. Furthermore, the polysaccharide structure has not been reported so far as deduced by the query on the Bacterial Carbohydrate Structure Database repository …”

“…As for Poly2,itisbuilt up of adisaccharide repeating unit made of l-rhamnose and d-fucose ( Figure 6), the latter being the less common fucose stereoisomer.F urthermore,t he polysaccharide structure has not been reported so far as deduced by the query on the Bacterial Carbohydrate Structure Database repository. [18] As for Poly1,its tricky architecture has been solved by an extensive and nontrivial integrated combination of chemical, spectroscopic,a nd computational methods.I ts monomeric unit consists of amonosaccharide,3OMe-d-Fuc4N,and an a- amino-acid derivative,( 2 'R,3'R,4'S) N-methyl-3',4'-dihydroxy-3'-methyl-5'-oxoproline,s ot hat the whole polymer alternates glycosidic and amidic linkages (Figure 3). From this perspective, Poly1 is unique because it is the first polymer whose repeating unit contains am onosaccharide and an aamino acid assembled together.T herefore,o ur view is that this O-antigen might be the first representative of anew class of natural polymers.…”

SweetOrigins: Extracting Evolutionary Information from Glycans

“…To create a comprehensive glycan dataset annotated with species labels, we manually curated 12,674 glycan sequences from three sources: UniCarbKB 41 , the Carbohydrate Structure Database (CSDB) 42 , and the peer-reviewed scientific literature. From UniCarbKB , we compiled all glycans with species information, a length of at least three monosaccharides, and a working link to PubChem.…”

Glycoinformatics: Bridging Isolated Islands in the Sea of Data

“…[13] Except for rare dedicated databases (such as Escherichia coli oriented ECODAB), [14] most of these databases deposit glycans of mammalian origin. Currently,C SDB [5] (which is developed by the authors of this Viewpoint) provides the most complete coverage on carbohydrates of prokaryotes.I t should be noted that none of the projects ensures the full coverage on natural carbohydrates,and only afew of them are curated. In the latter projects,only new entries,but not those imported from CarbBank, are verified (the only exclusions being CSDB and UniCarbKB,w hich claim to be fully curated).…”

“…Them ain goals of glycoinformatics include:1)providing scientists with the means of accessing the accumulated data on natural carbohydrates and of their statistical processing;2 )modeling various physicochemical, chemical, and biological properties of carbohydrates;3 )predicting carbohydrate structures on the basis of their properties;4 )formalizing the experimental protocols and arrangement of raw experimental data in glycochemistry and glycobiology.N owadays,w eh ave several carbohydrate databases that store structures of mammalian (Glycosciences.de, [2] UniCarbKB, [3] KEGG Glycan, [4] etc. ), plant, fungal, and bacterial (CSDB [5] )o rigins.S ince any separate project cannot cover all data and all types of services,bridging them with each other and with other life-science databases will promote all aspects of carbohydrate research, thus allowing services and tools from any project to access data from all other projects.The above-listed databases have been partially linked through al ocal triplet storage populated with Resource Description Framework feeds from individual participants. [6] However,u sage of this semantic web in everyday research is not astraightforward procedure for non-informaticians:i tr equires programming to solve new problems and depends on periodic updates from participant databases.…”