Carbohydrate Structure Database: Difference between revisions

Revision as of 13:58, 21 January 2019

Revision as of 02:51, 5 February 2019

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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 & Cellular Proteomics |volume=12|issue=4 |pages=1036–1045 |title=Using databases and web resources for glycomics research|doi=10.1074/mcp.R112.026252|PMID=23325765|pmc=3617328}}</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 |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 |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 |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 |title=Databases for Microbiologists|doi=10.1128/JB.00330-15|PMID=26013493|pmc=4505447}}</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 |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 |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 |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 |title=Cell surface of Lactococcus lactis is covered by a protective polysaccharide pellicle|doi=10.1074/jbc.M109.082958|PMID=20106971|pmc=2856253}}</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 Opinion in Structural Biology |volume=40 |pages=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 |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., |display-authors=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., |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}}</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}}</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}}</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=L&uuml;tteke 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}}</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=L&uuml;tteke 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==