CSDB: credits

The Plant & Fungal CSDB team is:
Philip Toukach, ScD, Assoc. Prof. management, system architecture,
programming, data verification
  Yuriy Knirel, ScD, Prof. general support






 Ksenia Egorova, PhD
Nadezhda Kalinchuk, PhD
Kirill Kazantsev, PhD
Ekaterina Belozertseva
Liza Shikina
Sofya Schcherbinina
Ekaterina Andreychuk		 manual literature processing,
data annotation and posting
Andrei Bochkov
Mikhail Dolgov		 programming
  Ivan Chernyshov
Roman Kapaev		 R&D, programming
currently active members

 

The first version of Plant & Fungal CSDB was deployed in 2014. Its core programs were developed within the Bacterial CSDB project.

The first pack of data was derived from the CCSD database (University of Georgia, Athens, USA, 1996) by retrospective error-checking and validation of data. The second pack was derived from local databases of multiple institutions of Russian Academy of Sciences. The main development center is N.D. Zelinksy Institute of Organic Chemistry (Moscow, Russia).

The project was supported by Russian Foundation for Basic Research grant N12-04-00324 (2012-2014).

 

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

 

Publications on Plant and Fungal CSDB:

Arabidopsis thaliana glycosyltransferase subdatabase:
(PMID 28011601, DOI 10.1093/glycob/cww137)
K.S Egorova, Ph.V. Toukach "CSDB_GT: a new curated database on glycosyltransferases", Glycobiology, 2017, 27(4): 285-290.

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.

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.

Other publications on CSDB:

Carbohydrate notations:
(PMID 31790229, DOI 10.1021/acs.jcim.9b00744)
Ph.V. Toukach, K.S. Egorova "New features of CSDB Linear, as compared to other carbohydrate notations", J Chem Inf Model, 2020, 60(3): 1276-1289.

Escherichia coli glycosyltransferases: (PMID 30759212, DOI 10.1093/glycob/cwz006)
K.S Egorova, Yu.A. Knirel, Ph.V. Toukach "Expanding CSDB_GT glycosyltransferase database with Escherichia coli", Glycobiology, 2019, 29(4): 285-287.

Essay on glycoinformatics:
(PMID 29786940, DOI 10.1002/anie.201803576)
K.S. Egorova, Ph.V. Toukach "Glycoinformatics: bridging isolated islands in the sea of data", Angewandte Chemie Intl Ed, 2018, 57(46): 14986-14990.

SMILES & 3D generation:
(PMID 29547883, DOI 10.1093/bioinformatics/bty168)
I.Yu. Chernyshov, Ph.V. Toukach "REStLESS: automated translation of glycan sequences from residue-based notation to SMILES and atomic coordinates", Bioinformatics, 2018, 34(15): 2679-2681.

NMR-based structure prediction:
(PMID 29092007, DOI 10.1093/bioinformatics/btx696)
R.R. Kapaev, Ph.V. Toukach "GRASS : semi-automated NMR-based structure elucidation of saccharides", Bioinformatics, 2018, 34(6): 957-963.

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 simulation 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.

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.

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.


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