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Line 36: }} '''Carbohydrate Structure Database (CSDB)''' is a free database and service platform in [[glycoinformatics]], launched in 2005<ref name="first">{{cite journal\| author=Toukach F.V.\|author2=Knirel Y.A.\| date=2005\|journal=Glycoconjugate Journal\|volume=22\|issue=4-6\|\|pages=~~216-217~~216–217\|title=New database of bacterial carbohydrate structures}}</ref> by a group of Russian scientists from [http://zioc.ru/?lang=en N.D. Zelinsky Institute of Organic Chemistry], Russian Academy of Sciences. CSDB stores structural and spectral data on natural [[carbohydrates]] and carbohydrate-related molecules. == 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~~><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}}</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 GODESS: glycan-oriented dual empirical spectrum simulation]).<ref name="GODESS">{{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="GODESS_1H">{{cite journal\| author=Kapaev R.R.\| author2=Toukach Ph.V.\|date=2015\|journal=Analytical Chemistry \|volume=87\|pages=~~7006-7010~~7006–7010 \|title=Improved carbohydrate structure generalization scheme for <sup>1</sup>H and <sup>13</sup>C NMR simulations\|doi=10.1021/acs.analchem.5b01413\|PMID=26087011}}</ref><ref name="GODESS_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~~1100–1104 \|title=Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software\|doi=10.1021/acs.jcim.6b00083\|PMID=27227420}}</ref> * Automated [[NMR]]-based structure elucidation ([http://csdb.glycoscience.ru/database/index.html?help=nmr#grass GRASS: generation, ranking and assignment of saccharide structures]). * [[Statistical analysis]] of structural feature distribution in [[glycomes]] of living organisms<ref name="taxon_clustering">{{cite journal\| author=Egorova K.S.\|author2=Kondakova A.N.\|author3=Toukach Ph.V.\| date=2015\|journal=Database \|pages=ID bav073 \|title=Carbohydrate structure database: tools for statistical analysis of bacterial, plant and fungal glycomes\|doi=10.1093/database/bav073\|PMID=26337239}}</ref><ref name="Statistics">{{cite journal\| author=Herget S.\| author2=Toukach Ph.V.\| author3=Ranzinger R.\| author4=Hull W.E.\| author5=Knirel Y.\| author6=von der Lieth C.-W.\| date=2008\|journal=BMC Structural Biology \|volume=8\|pages=ID 35 \|title=Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): Characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans\|doi=10.1186/1472-6807-8-35\|PMID=18694500}}</ref> Line 56: The main sources of CSDB data are: * Scientific publications indexed in the dedicated citation databases, including [https://www.ncbi.nlm.nih.gov/pubmed/ NCBI Pubmed] and [http://webofknowledge.com/ Thomson Reuters Web Of Science] (approx. 14000 records). * CCSD (Carbbank <ref>{{cite journal\|author=Doubet S.\|author2=Albersheim P.\| date=1992\|journal=Glycobiology\|volume=2\|issue=6 \|pages=~~505-507~~505–507 \|title=CarbBank\|PMID=1472756}}</ref>) database (approx. 3000 records). The data are selected and added to CSDB manually by browsing original scientific publications. The data originating from other databases are subject to error-correction and approval procedures .<ref name="Critical">{{cite journal\| author=Egorova K.S.\| author2=Toukach Ph.V.\| date=2012\|journal=Journal of Chemical Information and Modeling \|volume=52\|pages=~~2812-2814~~2812–2814 \|title=Critical analysis of CCSD data quality\|doi=10.1021/ci3002815\|PMID=23025661}}</ref>. As of the beginning of 2017, the coverage on [[bacteria]] and [[archaea]] is ca. 80% of carbohydrate structures published in scientific literature in the years 1943 - 2015.<ref name="Merged_CSDB"/> The time lag between the publication of relative data and their deposition into CSDB is about 18 months. Plants are covered up to 1997, and fungi up to 2005. <ref name="PFCSDB">{{cite journal\| author=Egorova K.S.\| author2=Toukach Ph.V.\| date=2013\|journal=Carbohydrate Research \|volume=389\|pages=~~112-114~~112–114\|title=Expansion of coverage of Carbohydrate Structure Database (CSDB)\|doi=10.1016/j.carres.2013.10.009\|PMID=24680503}}</ref>. CSDB does not cover data from the [[animalia]] ___domain, except [[Protozoa\|unicellular metazoa]]. There is a number of dedicated databases on [[animal]] [[carbohydrates]], e.g. [http://www.unicarbkb.org/ UniCarbKB] <ref name="unicarbkb">{{cite journal\|author=Campbell M.P.\|author2=Packer N.H. \| date=2016\|journal=Biochimica et biophysica acta \|volume=1860\|issue=8 \|pages=~~1669-1675~~1669–1675 \|title=UniCarbKB: New database features for integrating glycan structure abundance, compositional glycoproteomics data, and disease associations\|doi=10.1016/j.bbagen.2016.02.016\|PMID=26940363}}</ref> or [http://glycosciences.de GLYCOSCIENCES.de] .<ref>{{cite journal\|author=Lütteke T.\|author2=Bohne-Lang A.\|author3=Loss A.\|author4=Goetz T.\|author5=Frank M.\|author6=von der Lieth C.-W.\| date=2006\|journal=Glycobiology\|volume=16\|issue=5 \|pages=71R-81R \|title=GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research\|doi=10.1093/glycob/cwj049\|PMID=16239495}}</ref>. CSDB is reported as one of the biggest projects in [[glycoinformatics]].<ref>{{cite journal\|author=Rigden D.J.\|author2=Fernández-Suárez X.M.\|author3=Galperin M.Y. \| date=2016\|journal=Nucleic Acids Research \|volume=44\|issue=D1 \|pages=D1-D6 \|title=The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection\|doi=10.1093/nar/gkv1356\|PMID=26740669}}</ref><ref>{{cite journal\|author=Aoki-Kinoshita K.F. \| date=2013\|journal=Molecular and Cellular Proteomics \|volume=12\|issue=4 \|pages=~~1036-1045~~1036–1045 \|title=Using databases and web resources for glycomics research\|doi=10.1074/mcp.R112.026252\|PMID=23325765}}</ref><ref>{{cite journal\|author=Frank M.\|author2=Schloissnig S. \| date=2010\|journal=Cellular and Molecular Life Sciences \|volume=67\|issue=16 \|pages=~~2749-2772~~2749–2772 \|title=Bioinformatics and molecular modeling in glycobiology.\|doi=10.1007/s00018-010-0352-4\|PMID=20364395}}</ref><ref>{{cite journal\|author=Artemenko N.V.\|author2=McDonald A.G.\|author3=Davey G.P.\|author4=Rudd P.M. \| date=2012\|journal=Methods in Molecular Biology \|volume=899 \|pages=~~325-350~~325–350 \|title=Databases and tools in glycobiology\|doi=10.1007/978-1-61779-921-1_21\|PMID=22735963}}</ref><ref>{{cite journal\|author=Lütteke T. \| date=2012\|journal=Beilstein Journal of Organic Chemistry \|volume=8 \|pages=~~915-929~~915–929 \|title=The use of glycoinformatics in glycochemistry\|doi=10.3762/bjoc.8.104\|PMID=23015842}}</ref><ref>{{cite journal\|author=Zhulin I.B. \| date=2015\|journal=Journal of Bacteriology \|volume=197\|issue=15 \|pages=~~2458-2467~~2458–2467 \|title=Databases for Microbiologists\|doi=10.1128/JB.00330-15\|PMID=26013493}}</ref><ref>{{cite journal\|author=Yamada K.\|author2=Kakehi K. \| date=2011\|journal=Journal of pharmaceutical and biomedical analysis \|volume=55\|issue=4 \|pages=~~702-727~~702–727 \|title=Recent advances in the analysis of carbohydrates for biomedical use\|doi=10.1016/j.jpba.2011.02.003\|PMID=21382683}}</ref> It is employed in structural studies of natural carbohydrates<ref>{{cite journal\| author=Fontana C.\|author2=Zaccheus M.\|author3=Weintraub A.\|author4=Ansaruzzaman M.\|author5=Widmalm G.\| date=2016\|journal=Carbohydrate Research \|volume=432 \|pages=~~41-49~~41–49 \|title=Structural studies of a polysaccharide from Vibrio parahaemolyticus strain AN-16000\|doi=10.1016/j.carres.2016.06.004\|PMID=27392309}}</ref><ref>{{cite journal\| author=Potekhina N.V.\|author2=Shashkov A.S.\|author3=Senchenkova S.N.\|author4=Dorofeeva L.V.\|author5=Evtushenko L.I.\| date=2012\|journal=Biochemistry (Moscow) \|volume=77 \|issue=11 \|pages=~~1294-1302~~1294–1302 \|title=Structure of hexasaccharide 1-phosphate polymer from Arthrobacter uratoxydans VKM Ac-1979(T) cell wall\|doi=10.1134/S0006297912110089\|PMID=23240567}}</ref><ref>{{cite journal\| author=Chapot-Chartier M.P.\|author2=Vinogradov E.\|author3=Sadovskaya I.\|author4=Andre G.\|author5=Mistou M.Y.\|author6=Trieu-Cuot P.\|author7=Furlan S.\|author8=Bidnenko E.\|author9=Courtin P.\|author10=Péchoux C.\|author11=Hols P.\|author12=Dufrêne Y.F.\|author13=Kulakauskas S.\| date=2010\|journal=Journal of Biological Chemistry \|volume=285\|issue=14 \|pages=~~10464-10471~~10464–10471 \|title=Cell surface of Lactococcus lactis is covered by a protective polysaccharide pellicle\|doi=10.1074/jbc.M109.082958\|PMID=20106971}}</ref> and in glyco-profiling.<ref>{{cite journal\| author=Walsh I.\|author2=Zhao S.\|author3=Campbell M.\|author4=Taron C.H.\|author5=Rudd P.M.\| date=2016\|journal=Current Opinions in Structural Biology \|volume=40 \|pages=~~70-80~~70–80 \|title=Quantitative profiling of glycans and glycopeptides: an informatics' perspective\|doi=10.1016/j.sbi.2016.07.022\|PMID=27522273}}</ref> The content of CSDB has been used as a data source in other [[glycoinformatics]] projects.<ref>{{cite journal\|author=Ranzinger R.\|author2=York W.S. \| date=2015\|journal=Methods in Molecular Biology \|volume=1273 \|pages=~~109-124~~109–124 \|title=GlycomeDB\|doi=10.1007/978-1-4939-2343-4_8\|PMID=25753706}}</ref><ref>{{cite journal\|author=Ranzinger R.\|author2=Herget S.\|author3=von der Lieth C.-W.\|author4=Frank M. \| date=2011\|journal=Nucleic Acids Research - Database Issue \|volume=39 \|pages=D373-376 \|title=GlycomeDB - a unified database for carbohydrate structures\|doi=10.1093/nar/gkq1014\|PMID=21045056}}</ref><ref>{{cite journal\|author=Aoki-Kinoshita K.F., et al. \| date=2016\|journal=Nucleic Acids Research - Database Issue \|volume=44\|issue=D1 \|pages=D1237-1242 \|title=GlyTouCan 1.0 - The international glycan structure repository\|doi=10.1093/nar/gkv1041\|PMID=26476458}}</ref><ref>{{cite journal\|author=Campbell M.P.\|author2=Ranzinger R.\|author3=Lütteke T.\|author4=Mariethoz J.\|author5=Hayes CA.\|author6=Zhang J.\|author7=Akune Y.\|author8=Aoki-Kinoshita K.F.\|author9=Damerell D.\|author10=Carta G.\|author11=York W.S.\|author12=Haslam S.M.\|author13=Narimatsu H.\|author14=Rudd P.M.\|author15=Karlsson N.G.\|author16=Packer N.H.\|author17=Lisacek F. \| date=2014\|journal=BMC Bioinformatics \|volume=15 \|pages=Suppl 1:S9 \|title=Toolboxes for a standardised and systematic study of glycans\|doi=10.1186/1471-2105-15-S1-S9\|PMID=24564482}}</ref> == 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\|doi=10.1186/1471-2105-9-384\|PMID=18803830}}</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 - Database Issue \|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\|doi=10.1093/nar/gkl883\|PMID=17202164}}</ref>, such as [http://www.monosaccharidedb.org MonosaccharideDB], [http://glycosciences.de Glycosciences.DE], [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], etc. Structures are presented in multiple carbohydrate notations (SNFG,<ref>{{cite journal\|author=Varki A., et al. \| date=2015\|journal=Glycobiology \|volume=25\|issue=12 \|pages=~~1323-1324~~1323–1324 \|title=Symbol Nomenclature for Graphical Representations of Glycans\|doi=10.1093/glycob/cwv091\|PMID=26543186}}</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~~405–408 \|title=SWEET-DB: an attempt to create annotated data collections for carbohydrates\|PMID=11752350}}</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~~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~~1558–1566 \|title=WURCS: the Web3 unique representation of carbohydrate structures\|doi=10.1021/ci400571e\|PMID=24897372}}</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~~622–655 \|title=GLYCAM06: a generalizable biomolecular force field. Carbohydrates\|doi=10.1002/jcc.20820\|PMID=17849372}}</ref>, etc.). CSDB is exportable as an [[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~~919–925\|title=GlycoRDF: An ontology to standardize Glycomics data in RDF\|doi=10.1093/bioinformatics/btu732\|PMID=25388145}}</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\|doi=10.1186/2041-1480-4-39\|PMID=24280648}}</ref> ==External links== * [http://csdb.glycoscience.ru CSDB web site] * [http://csdb.glycoscience.ru/database/core/help.php?db=database&topic=examples CSDB usage examples]

Carbohydrate Structure Database: Difference between revisions