Carbohydrate Structure Database: Difference between revisions

Revision as of 18:15, 7 May 2021

Revision as of 18:57, 8 November 2021

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|organism = {{unbulleted list | [[archaea]], [[bacteria]], [[fungi]], [[algae]], [[higher plants]]}}

|center = Zelinsky Institute of Organic Chemistry

|citation = Carbohydrate Structure Database <ref name="Merged_CSDB">{{cite journal| author=Toukach Ph.V.| author2=Egorova K.S.| date=2016|journal= Nucleic Acids Research - Database Issue |volume=44|issue=D1|pages=D1229–D1236 |title=Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts|doi=10.1093/nar/gkv840|pmid=26286194|pmc=4702937}}</ref>

|laboratory =

|author = Philip V. Toukach, Ksenia S. Egorova, Yuri A. Knirel, et al.

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==History and funding==

Until 2015, [http://csdb.glycoscience.ru/bacterial/index.html Bacterial Carbohydrate Structure Database] (BCSDB) and [http://csdb.glycoscience.ru/plant_fungal/index.html Plant&Fungal Carbohydrate Structure Database] (PFCSDB) databases existed in parallel. In 2015, they were joined into the single [http://csdb.glycoscience.ru/database/index.html Carbohydrate Structure Database] (CSDB).<ref name="Merged_CSDB">{{cite journal| author=Toukach Ph.V.| author2=Egorova K.S.| date=2016|journal=Nucleic Acids Research - Database Issue |volume=44|issue=D1|pages=D1229–D1236 |title=Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts|doi=10.1093/nar/gkv840|pmid=26286194|pmc=4702937}}</ref> The development and maintenance of CSDB have been funded by [http://www.istc.int/en/ International Science and Technology Center] (2005-2007), [http://grants.extech.ru Russian Federation President grant program] (2005-2006), [http://www.rfbr.ru/rffi/eng Russian Foundation for Basic Research] (2005-2007,2012-2014,2015-2017,2018-2020), [https://www.dkfz.de/ Deutsches Krebsforschungszentrum] (short-term in 2006-2010), and [https://www.rscf.ru/en/ Russian Science Foundation] (2018-2020).

== Data sources and coverage ==

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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|volume=1860|issue=8 |pages=1669–1675 |title=UniCarbKB: New database features for integrating glycan structure abundance, compositional glycoproteomics data, and disease associations|journal=Biochimica et Biophysica Acta (BBA) - General Subjects |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|doi-access=free}}</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 |pmc=4702933}}</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 |pmc=2912727}}</ref><ref>{{cite book|author=Artemenko N.V.|author2=McDonald A.G.|author3=Davey G.P.|author4=Rudd P.M. | date=2012|series=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|isbn=978-1-61779-920-4}}</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 |pmc=3388882}}</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|url=http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-133271}}</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|s2cid=9699031}}</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|doi-access=free}}</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 book|author=Ranzinger R.|author2=York W.S. | date=2015|series=Methods in Molecular Biology |volume=1273 |pages=109–124 |title=GlycomeDB|doi=10.1007/978-1-4939-2343-4_8|pmid=25753706|isbn=978-1-4939-2342-7 }}</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|issue=Database issue|doi=10.1093/nar/gkq1014|pmid=21045056 |pmc=3013643}}</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 |pmc=4702779}}</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 |pmc=4016020}}</ref>

==Deposited objects==

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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|doi=10.1186/1471-2105-9-384|pmid=18803830 |pmc=2567997}}</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|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], [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}}</ref>

==External links==