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词条 Carbohydrate Structure Database
释义

  1. Overview

  2. History and funding

  3. Data sources and coverage

  4. Interrelation with other databases

  5. External links

  6. References

{{infobox biodatabase
|title = Carbohydrate Structure Database
|logo =
|description = Natural carbohydrate structures with NMR, bibliographic and biological annotations.
|scope = carbohydrate structures and related data
|organism = {{unbulleted list | archaea, bacteria, fungi, algae, higher plants}}
|center = Zelinsky Institute of Organic Chemistry
|citation = Carbohydrate Structure Database [1]
|laboratory =
|author = Philip V. Toukach, Yuri A. Knirel et al.
|pmid =
|released = 2005
|standard =
|format =
|url = http://csdb.glycoscience.ru/
|download = export feature in web-interface
|webservice =
|sql =
|sparql =
|webapp = {{Plainlist|
  • GODDESS: glycan-oriented NMR spectrum simulation
  • GRASS: generation, ranking and assignment of saccharide structures
  • Coverage statistics
  • Taxon clustering
  • GT-explorer

}}
|standalone =
|license =
|versioning = yes
|frequency = annual
|curation = yes (manual and automatic)
|bookmark =
|version=1 (merged)
}}

Carbohydrate Structure Database (CSDB) is a free database and service platform in glycoinformatics, launched in 2005[2] by a group of Russian scientists from N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences. CSDB stores published structural, taxonomical, bibliographic and NMR-spectroscopic 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 NMR spectra, information on methods used to decipher a particular structure, and some other data.[1][3]

CSDB provides access to several carbohydrate-related research tools:

  • Simulation of 1D and 2D NMR spectra of carbohydrates (GODESS: glycan-oriented dual empirical spectrum simulation).[4][5][6]
  • Automated NMR-based structure elucidation (GRASS: generation, ranking and assignment of saccharide structures).[7]
  • Statistical analysis of structural feature distribution in glycomes of living organisms[8][9]
  • Generation of optimized atomic coordinates for an arbitrary saccharide[10]
  • Taxon clustering based on similarities of glycomes (carbohydrate-based tree of life)[8]
  • Glycosyltransferase subdatabase (GT-explorer)[11]

History and funding

Until 2015, Bacterial Carbohydrate Structure Database (BCSDB) and Plant&Fungal Carbohydrate Structure Database (PFCSDB) databases existed in parallel. In 2015, they were joined into the single Carbohydrate Structure Database (CSDB).[12] The development and maintenance of CSDB have been funded by International Science and Technology Center (2005-2007), Russian Federation President grant program (2005-2006), Russian Foundation for Basic Research (2005-2007,2012-2014,2015-2017), and Deutsches Krebsforschungszentrum (short-term in 2006-2010).

Data sources and coverage

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 Thomson Reuters Web Of Science (approx. 14000 records).
  • CCSD (Carbbank [13]) 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.[14]

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.[1] 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.[15]

CSDB does not cover data from the animalia domain, except unicellular metazoa. There is a number of dedicated databases on animal carbohydrates, e.g. UniCarbKB [16] or GLYCOSCIENCES.de.[17]

CSDB is reported as one of the biggest projects in glycoinformatics.[18][19][20][21][22][23][24] It is employed in structural studies of natural carbohydrates[25][26][27] and in glyco-profiling.[28]

The content of CSDB has been used as a data source in other glycoinformatics projects.[29][30][31][32]

Interrelation with other databases

CSDB is cross-linked to other glycomics databases,[33][34] such as MonosaccharideDB, 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,[35] SweetDB,[36] GlycoCT,[37] WURCS,[38] GLYCAM,[39] etc.). CSDB is exportable as a Resource Description Framework (RDF) feed according to the [https://bioportal.bioontology.org/ontologies/GLYCORDF GlycoRDF] ontology.[40][41]

External links

  • CSDB web site
  • CSDB usage examples
  • CSDB technical documentation
  • CSDB Linear (structure encoding notation)
  • [https://www.oxfordjournals.org/nar/database/subcat/4/12 Carbohydrate databases registered in NAR collection]
  • Carbohydrate databases in the recent decade (lection)

References

1. ^1 2 {{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}}
2. ^{{cite journal| author=Toukach F.V.|author2=Knirel Y.A.| date=2005|journal=Glycoconjugate Journal|volume=22|issue=4-6|pages=216–217|title=New database of bacterial carbohydrate structures}}
3. ^{{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}}
4. ^{{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}}
5. ^{{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 1H and 13C NMR simulations|doi=10.1021/acs.analchem.5b01413|PMID=26087011}}
6. ^{{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 GODESS Software|doi=10.1021/acs.jcim.6b00083|PMID=27227420}}
7. ^{{cite journal| author=Kapaev R.R.| author2=Toukach Ph.V.|date=2018|journal=Bioinformatics |volume=34|issue=6|pages=957–963 |title=GRASS: semi-automated NMR-based structure elucidation of saccharides|doi = 10.1093/bioinformatics/btx696|PMID=29092007}}
8. ^1 {{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}}
9. ^{{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}}
10. ^{{cite journal| author=Chernyshov I.Y.| author2=Toukach Ph.V.|date=2018|journal=Bioinformatics |title=REStLESS: Automated Translation of Glycan Sequences from Residue-Based Notation to SMILES and Atomic Coordinates|doi = 10.1093/bioinformatics/bty168|PMID=29547883}}
11. ^{{cite journal| author= Toukach Ph.V.| author2=Egorova K.S. |date=2016|journal=Glycobiology |volume=in production|title=CSDB_GT: a new curated database on glycosyltransferases|doi=10.1093/glycob/cww137}}
12. ^{{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}}
13. ^{{cite journal|author=Doubet S.|author2=Albersheim P.| date=1992|journal=Glycobiology|volume=2|issue=6 |pages=505–507 |title=CarbBank|PMID=1472756}}
14. ^{{cite journal| author=Egorova K.S.| author2=Toukach Ph.V.| date=2012|journal=Journal of Chemical Information and Modeling |volume=52|pages=2812–2814 |title=Critical analysis of CCSD data quality|doi=10.1021/ci3002815|PMID=23025661}}
15. ^{{cite journal| author=Egorova K.S.| author2=Toukach Ph.V.| date=2013|journal=Carbohydrate Research |volume=389|pages=112–114|title=Expansion of coverage of Carbohydrate Structure Database (CSDB)|doi=10.1016/j.carres.2013.10.009|PMID=24680503}}
16. ^{{cite journal|author=Campbell M.P.|author2=Packer N.H. | date=2016|journal=Biochimica et Biophysica Acta |volume=1860|issue=8 |pages=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}}
17. ^{{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}}
18. ^{{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}}
19. ^{{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}}
20. ^{{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}}
21. ^{{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}}
22. ^{{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}}
23. ^{{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}}
24. ^{{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}}
25. ^{{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}}
26. ^{{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}}
27. ^{{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}}
28. ^{{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}}
29. ^{{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}}
30. ^{{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}}
31. ^{{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}}
32. ^{{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}}
33. ^{{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}}
34. ^{{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}}
35. ^{{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}}
36. ^{{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}}
37. ^{{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}}
38. ^{{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}}
39. ^{{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}}
40. ^{{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}}
41. ^{{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}}
42. ^{{cite journal| author=Toukach Ph.V.| date=2013|journal=Glycoconjugate Journal |volume=30|pages=347-349 |title=CSDB and other carbohydrate databases}}

4 : Biological databases|Carbohydrates|Chemical databases|Glycomics
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