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{{External links|date=March 2024}}
{{infobox biodatabase
|title = Carbohydrate Structure Database
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== Overview ==
The main data stored in CSDB are [[carbohydrate]] structures of bacterial, fungal, and plant origin. Each structure is assigned to an organism and is provided with the link(s) to the corresponding scientific publication(s), in which it was described. Apart from structural data, CSDB also stores [[Nuclear Magnetic Resonance Spectroscopy|NMR]] spectra, information on methods used to decipher a particular structure, and some other data.<ref name="Merged_CSDB" /><ref>{{cite journal| author=Harvey D.J.| date=2015|journal=Mass Spectrometry Reviews |title=Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012|doi=10.1002/mas.21471|pmid=26270629|volume=36| issue=3|pages=255–422| url=https://ora.ox.ac.uk/objects/uuid:8c8d3748-8a59-4bde-96cf-a1788d258885}}</ref>
CSDB provides access to several carbohydrate-related research tools:
* Simulation of 1D and 2D [[NMR]] spectra of [[carbohydrates]] ([http://csdb.glycoscience.ru/database/index.html?help=nmr GODDESS: glycan-oriented database-driven empirical spectrum simulation]).<ref name="GODDESS">{{cite journal| author=Kapaev R.R.| author2=Egorova K.S.| author3=Toukach Ph.V.|date=2014|journal=Journal of Chemical Information and Modeling |volume=54|issue=9|pages=2594–2611 |title=Carbohydrate structure generalization scheme for database-driven simulation of experimental observables, such as NMR chemical shifts|doi = 10.1021/ci500267u|pmid=25020143}}</ref><ref name="GODDESS_1H">{{cite journal| author=Kapaev R.R.| author2=Toukach Ph.V.|date=2015|journal=Analytical Chemistry |volume=87|pages=7006–7010 |title=Improved carbohydrate structure generalization scheme for <sup>1</sup>H and <sup>13</sup>C NMR simulations| issue=14|doi=10.1021/acs.analchem.5b01413|pmid=26087011}}</ref><ref name="GODDESS_2D">{{cite journal| author=Kapaev R.R.| author2=Toukach Ph.V.|date=2016|journal=Journal of Chemical Information and Modeling |volume=56|pages=1100–1104 |title=Simulation of 2D NMR Spectra of Carbohydrates Using GODDESS Software| issue=6|doi=10.1021/acs.jcim.6b00083|pmid=27227420}}</ref>
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== Interrelation with other databases ==
CSDB is cross-linked to other [[glycomics]] databases,<ref>{{cite journal| author=Ranzinger R.|author2=Herget S.|author3=Wetter T.|author4=von der Lieth C.-W.| date=2008|journal=BMC Bioinformatics |volume=9 |pages=ID 384 |title=GlycomeDB - integration of open-access carbohydrate structure databases|article-number=384 |doi=10.1186/1471-2105-9-384|pmid=18803830 |pmc=2567997 |doi-access=free }}</ref><ref name="Integration_1">{{cite journal| author=Toukach Ph.V.|author2=Joshi H.| author3=Ranzinger R.| author4=Knirel Y.| author5=von der Lieth C.-W.| date=2007|journal=Nucleic Acids Research|volume=35|pages=D280–D286|title=Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de|issue=Database issue|doi=10.1093/nar/gkl883|pmid=17202164| pmc=1899093}}</ref> such as [http://www.monosaccharidedb.org MonosaccharideDB], [http://glycosciences.de Glycosciences.DE] {{Webarchive|url=https://web.archive.org/web/20210211160118/http://www.glycosciences.de/ |date=2021-02-11 }}, [https://www.ncbi.nlm.nih.gov/pubmed/ NCBI Pubmed], [https://www.ncbi.nlm.nih.gov/taxonomy NCBI Taxonomy], [https://www.ncbi.nlm.nih.gov/nlmcatalog NLM catalog], [https://www.who.int/classifications/icd/en/ International Classification of Diseases 11], etc. Besides a native notation, CSDB Linear,<ref>{{cite journal|author=Toukach Ph.V.|author2=Egorova K.S.| date=2020|journal=Journal of Chemical Information and Modeling |volume=60|issue=3 |pages=1276–1289 |title=New features of CSDB Linear, as compared to other carbohydrate notations|doi= 10.1021/acs.jcim.9b00744|pmid=31790229|s2cid=226214957}}</ref> structures are presented in multiple carbohydrate notations (SNFG,<ref>{{cite journal|author=Varki A.|display-authors=et al | date=2015|journal=Glycobiology |volume=25|issue=12 |pages=1323–1324 |title=Symbol Nomenclature for Graphical Representations of Glycans|doi=10.1093/glycob/cwv091|pmid=26543186|pmc=4643639}}</ref> SweetDB,<ref>{{cite journal|author=Loss A.|author2=Bunsmann P.|author3=Bohne A.|author4=Loss A.|author5=Schwarzer E.|author6=Lang E.|author7=von der Lieth C.-W. | date=2002|journal=Nucleic Acids Research |volume=30|issue=1 |pages=405–408 |title=SWEET-DB: an attempt to create annotated data collections for carbohydrates|pmid=11752350 |doi=10.1093/nar/30.1.405 |pmc=99123}}</ref> GlycoCT,<ref>{{cite journal|author=Herget S.|author2=Ranzinger R.|author3=Maass K.|author4=von der Lieth C.-W.| date=2008|journal=Carbohydrate Research |volume=343|issue=12 |pages= 2162–2171|title=GlycoCT - a unifying sequence format for carbohydrates|doi=10.1016/j.carres.2008.03.011|pmid=18436199}}</ref> [http://www.wurcs-wg.org WURCS],<ref>{{cite journal|author=Tanaka K.|author2=Aoki-Kinoshita K.F.|author3=Kotera M.|author4=Sawaki H.|author5=Tsuchiya S.|author6=Fujita N.|author7=Shikanai T.|author8=Kato M.|author9=Kawano S.|author10=Yamada I.|author11=Narimatsu H. | date=2014|journal=Journal of Chemical Information and Modeling |volume=54|issue=6 |pages=1558–1566 |title=WURCS: the Web3 unique representation of carbohydrate structures|doi=10.1021/ci400571e|pmid=24897372|doi-access=free}}</ref> [http://glycam.org GLYCAM],<ref>{{cite journal|author=Kirschner K.N.|author2=Yongye A.B.|author3=Tschampel S.M.|author4=González-Outeiriño J.|author5=Daniels C.R.|author6=Foley B.L.|author7=Woods R.J. | date=2008|journal=Journal of Computational Chemistry |volume=29|issue=4 |pages=622–655 |title=GLYCAM06: a generalizable biomolecular force field. Carbohydrates|doi=10.1002/jcc.20820|pmid=17849372|pmc=4423547}}</ref> etc.). CSDB is exportable as a [[Resource Description Framework]] (RDF) feed according to the [https://bioportal.bioontology.org/ontologies/GLYCORDF GlycoRDF] ontology.<ref name="Ontology">{{cite journal| author=Ranzinger R.| author2=Aoki-Kinoshita K.F.| author3=Campbell M.P.| author4=Kawano S.| author5=Lütteke T.| author6=Okuda S.| author7=Shinmachi D.| author8=Shikanai T.| author9=Sawaki H.| author10=Toukach Ph.V.| author11=Matsubara M.| author12=Yamada I.| author13=Narimatsu H.|date=2015|journal=Bioinformatics|volume=31|issue=6|pages=919–925|title=GlycoRDF: An ontology to standardize Glycomics data in RDF|doi=10.1093/bioinformatics/btu732|pmid=25388145| pmc=4380026}}</ref><ref name="Integration_2">{{cite journal| author=Aoki-Kinoshita K.F.| author2=Bolleman J.| author3=Campbell M.P.| author4=Kawano S.| author5=Kim J.| author6=Lütteke T.| author7=Matsubara M.| author8=Okuda S.| author9=Ranzinger R.| author10=Sawaki H.| author11=Shikanai T.| author12=Shinmachi D.| author13=Suzuki Y.| author14=Toukach Ph.V.| author15=Yamada I.| author16=Packer N.H.| author17=Narimatsu H.| date=2013|journal=Journal of Biomedical Semantics |volume=4|pages=ID 39 |title=Introducing glycomics data into the Semantic Web| issue=1|doi=10.1186/2041-1480-4-39|pmid=24280648| pmc=4177142| doi-access=free}}</ref>
==External links==
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