CSDB: credits

The Bacterial CSDB team is/was:
Yuriy Knirel, Prof. management, data verification
Philip Toukach, Assoc. Prof. management, system architecture,
programming, data verification
Nadezhda Kalinchuk, PhD
Stella Khalfina
Evelina Zdorovenko, PhD
Andrey Perepelov, PhD
Anna Kondakova, PhD
Olga Ovchinnikova, PhD
N. Chekareva, PhD
manual literature processing,
data posting
Ksenia Egorova, PhD data verification
  A. Anisimov, ScD pilot project sub-management
  Dmitry Dmitriev
Ivan Bushmarinov, PhD
pilot project programming
  Olga Bystrova, PhD
Nina Kocharova, PhD
Leon Backinowsky, Prof. †
Sofya Senchenkova, PhD
workshop organisation
 
Mikhail Dolgov
Roman Kapaev
programming
  Claus-Willi von der Lieth, Prof. †
Thomas Lütteke, Prof.
Stephan Herget, PhD
Rene Ranzinger
colsultations and critics
  Pavel Belyakov, PhD † server administration
currently active members

 

The first version of BCSDB (CSBD-II) was developed within the framework of the International Science and Technology Center Partner Project grant #1197, supported by the Cooperative Threat Reduction Program of the US Department of Defense (ISTC Partner).

The data came from the Carbbank database created in the University of Georgia (Athens, USA) and the local database of the Carbohydrate Chemistry Lab of N.D. Zelinksy Institute of Organic Chemistry (Moscow, Russia).

Later, the project had been supported by Russian Foundation for Basic Research grant N05-07-90099, Russian Federation President program grant MK-1700.2005.4 and Deutsches Krebsforschungszentrum (Heidelberg, Germany) short-term guest scientistship stipendia in 2006-2009.

 

Questions, proposals and bug reports can be addresed to Philip Toukach.

 

Publications on Bacterial CSDB:

Two book chapters on daily usage of CSDB with examples:
(DOI 10.1007/978-1-4939-2343-4_5, online ISBN 978-1-4939-2343-4, print ISBN 978-1-4939-2342-7)
Ph. Toukach, K. Egorova "Bacterial, Plant, and Fungal Carbohydrate Structure Databases: daily usage", in "Glycoinformatics", eds: T. Lütteke, M. Frank, series: Methods in Molecular Biology, v. 1273. Springer New York, 2015, ch.5, pp. 55-85. (DOI 10.1007/978-4-431-54841-6_24, online ISBN 978-4-431-54836-2, print ISBN 978-4-431-54840-9)
Ph. Toukach, K. Egorova "Bacterial, Plant, and Fungal Carbohydrate Structure Database (CSDB)", in "Glycoscience: Biology and Medicine", eds: T. Endo, P.H. Seeberger, G.W. Hart, C-H. Wong, N. Taniguchi, Springer Japan, 2014, ch. 29, pp. 241-250.

Main paper: database control programs, interface and comparison of existing databases: (PMID 21155523, DOI 10.1021/ci100150d)
Ph. Toukach "Bacterial Carbohydrate Structure Database 3: principles and realization", J Chem Inf Model 2011, 51(1): 159-170.

Comparative analysis of database content: (PMID 18694500, DOI 10.1186/1472-6807-8-35)
S. Herget, Ph. Toukach, R. Ranzinger, W.E. Hull, Y. Knirel, C.-W. von der Lieth "Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): Characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans", BMC Struct Biol 2008, 8: 35.

First report on cross-database interaction in glycoscience: (PMID 17202164, DOI 10.1093/nar/gkl883)
Ph. Toukach, H. Joshi, R. Ranzinger, Yu. Knirel, C.-W. von der Lieth "Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de", Nucleic Acids Res - Database Issue, 2007, 35: D280-D286.

First presentation:
F.V. Toukach, Y.A. Knirel "New database of bacterial carbohydrate structures", Glycoconjugate J, 2005, 22: 216-217.

Other publications on CSDB:

Glycosyltransferase subdatabase:
( DOI 10.1093/glycob/cww109)
K.S Egorova, Ph.V. Toukach "CSDB_GT : a new curated database on glycosyltransferases", Glycobiology, 2016, in press.

Overview of the merged CSDB:
(PMID 262861940, DOI 10.1093/nar/gkv840)
Ph.V. Toukach, K.S Egorova "Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts", Nucleic Acids Res - Database Issue, 2015, 44(D1): D1229-D1236.

Statistical studies of CSDB content and taxon clustering:
(PMID 26337239, DOI 10.1093/database/bav073)
K.S Egorova, A.N. Kondakova, Ph.V. Toukach "Carbohydrate structure database: tools for statistical analysis of bacterial, plant and fungal glycomes", Database, 2015, ID bav073.

Three papers on CSDB NMR prediction service:
(PMID 27227420, DOI 10.1021/acs.jcim.6b00083)
R.R. Kapaev, Ph.V. Toukach "Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software", J Chem Inf Model, 2016, 56(6): 1100-1104.
(PMID 25020143, DOI 10.1021/ci500267u)
R.R. Kapaev, K.S. Egorova, Ph.V. Toukach "Carbohydrate structure generalization scheme for database-driven simulation of experimental observables, such as NMR chemical shifts", J Chem Inf Model, 2014, 54: 2594-2611.
(PMID 26087011, DOI 10.1021/acs.analchem.5b01413)
R.R. Kapaev, Ph.V. Toukach "Improved carbohydrate structure generalization scheme for 1H and 13C NMR simulations.", Anal Chem, 2015, 87: 7006-7010.

Presentation of Plant and Fungal CSDB: (PMID 24680503, DOI 10.1016/j.carres.2013.10.009)
K.S. Egorova, Ph.V. Toukach "Expansion of coverage of Carbohydrate Structure Database (CSDB)", Carbohydr Res, 2014, 389: 112-114.

Three papers on cross-database integration in glycomics:
(PMID 24190976, DOI 10.1093/glycob/cwt084)
K.F. Aoki-Kinoshita et al. "The fifth ACGG-DB meeting report: Towards an international glycan structure repository", Glycobiology 2013, 23: 1422-1424.
(PMID 24280648, DOI 10.1186/2041-1480-4-39)
K.F. Aoki-Kinoshita, J. Bolleman, M.P. Campbell, S. Kawano, J. Kim, T. Lütteke, M. Matsubara, S. Okuda, R. Ranzinger, H. Sawaki, T. Shikanai, D. Shinmachi, Y. Suzuki, Ph.V. Toukach, I. Yamada, N.H. Packer, H. Narimatsu "Introducing glycomics data into the Semantic Web", J Biomed Semantics 2013, 4: 39.
(PMID 25388145, DOI 10.1093/bioinformatics/btu732)
R. Ranzinger, K.F. Aoki-Kinoshita, M.P. Campbell, S. Kawano, T. Lütteke, S. Okuda, D. Shinmachi, T. Shikanai, H.Sawaki, Ph.V. Toukach, M. Matsubara, I. Yamada, H. Narimatsu "GlycoRDF: An ontology to standardize Glycomics data in RDF", Bioinformatics 2015, 31(6): 919-925.

Mini-review on existing carbohydrate databases:
Ph.V. Toukach "CSDB and other carbohydrate databases", Glycoconjugate J, 2013, 30: 347-349.

Carbbank data validation within CSDB: (PMID 23025661, DOI 10.1021/ci3002815)
K.S. Egorova, Ph.V. Toukach "Critical analysis of CCSD data quality", J Chem Inf Model, 2012, 52: 2812-2814.



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