CSDB: credits

The CSDB team is/was:
	Philip Toukach, ScD, Assoc. Prof.	Bacterial, Plant&Fungal, GT: management, research&development, programming, data verification
	Yuriy Knirel, ScD, Prof.	Bacterial: data verification general support Pilot project: management
	Ksenia Egorova, ScD	Bacterial, Plant&Fungal, GT: manual literature processing, data verification Services: statistics
	Nadezhda Kalinchuk, PhD	Bacterial, Plant&Fungal: manual literature processing, data annotation and posting
	Kirill Kazantsev, PhD Ekaterina Belozertseva Liza Shikina Sofya Shcherbinina Ekaterina Andreychuk	Plant&Fungal: manual literature processing, data annotation and posting
	Nadezhda Smirnova, PhD Anastasia Shirkovskaya	GT: manual literature processing, data annotation
	Ivan Chernyshov Roman Kapaev	Services: research&development, programming
	Andrei Bochkov Mikhail Dolgov	Services: programming
	Stella Khalfina Evelina Zdorovenko, PhD Andrey Perepelov, PhD Anna Kondakova, PhD	Bacterial: data annotation and posting
	A. Anisimov, ScD	Pilot project: sub-management
	Dmitry Dmitriev Ivan Bushmarinov, PhD	Pilot project: programming
	Olga Bystrova, PhD Nina Kocharova, PhD Leon Backinowsky, ScD, Prof. † Sofya Senchenkova, PhD	Pilot project: workshop organization
	Pavel Belyakov, PhD † Alexander Shushpanov	server administration
	Claus-Willi von der Lieth, Prof. † Thomas Lütteke, Prof. Kiyoko Aoki-Kinoshita, Prof. Stephan Herget, PhD Rene Ranzinger, PhD	colsultations and critics
currently active members

Acknowledgements

The first version of Bacterial CSDB was deployed in 2005 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 first version of Plant&Fungal CSDB was deployed in 2013 with the use of core programs from Bacterial CSDB. Later, the project has been supported by Russian Foundation for Basic Research grants N05-07-90099 (2005-2007), N12-04-00324 (2012-2014), N15-04-01065 (2015-2017), and N18-04-00094 (2018-2020), Russian Science Foundation grant N18-14-00098 (2018-2020, prolonged 2021-2022), Russian Federation President program grant MK-1700.2005.4 (2005-2006) and Deutsches Krebsforschungszentrum (Heidelberg, Germany) short-term guest scientistship stipendia (2006-2009).

The first pack of data was derived from the CCSD (Carbbank) database (University of Georgia, Athens, USA) by retrospective error-checking and validation of data. The second pack was derived from annotation of publications from the local bibliographic database of the Carbohydrate Chemistry Lab of N.D. Zelinksy Institute of Organic Chemistry (Moscow, Russia) and other institutions of Russian Academy of Sciences. The biggest third pack originates from our own annotation and curation efforts on publications selected from Web Of Science and NCBI Pubmed databases.

The Bacterial (BCSDB) and Plant&Fungal (PFCSDB) databases were merged in 2015 to improve the quality of content-dependent services, such as taxon clustering and NMR simulation.

Citing and feedback

On CSDB usage, please, cite the appropriate papers from the list below, e.g.:

• General CSDB [14,15,19,20]
• Usage of bacterial or archaeal data [32]
• Usage of plant or fungal data [18,26]
• Usage of glycosyltransferase data [10,11,12]
• Usage of conformation data [2,3,4]
• Usage of glycoepitope data [13]
• Usage of raw CSDB data in an own project [5]
• SMILES & 3D generation [8]
• Carbohydrate notations [7]
• Structure editor, 3D modeler and GlycoCT translation [6]
• NMR simulation and structure prediction [9,22,23,24]
• Statistical analysis of glycomes [16,17,18]
• Automated interaction with CSDB [21,28,33]
• Data quality and remediation [30,31]
• Glycoinformatics (and CSDB in historical context) [1,34]

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

Publications

Essay on glycoinformatics:

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

   Three papers on 3D structures in CSDB and other databases:

2. S.I. Shcherbinina, Ph.V. Toukach "Three-dimensional structures of carbohydrates and where to find them", Int J Mol Sci, 2020, 21(20): ID 7702. (PMID 33081008, DOI 10.3390/ijms21207702)
3. V.S. Stroylov, M.P.Panova, Ph.V. Toukach "Comparison of methods for bulk automated simulation of glycosidic bond conformations", Int J Mol Sci, 2020, 21(20): ID 7626. (PMID 33076365, DOI 10.3390/ijms21207626)
4. S.I. Scherbinina, M. Frank, Ph.V. Toukach "Carbohydrate Structure Database (CSDB) oligosaccharide conformation tool", Glycobiology, 2021, 32(6): 460-468. (PMID 35275211, DOI 10.1093/glycob/cwac011)

   CSDB source data:

5. Ph.V. Toukach, K.S. Egorova "Source files of the Carbohydrate Structure Database: the way to sophisticated analysis of natural glycans", Scientific Data, 2022, 9: ID 131. (PMID 35354826, DOI 10.1038/s41597-022-01186-9)

   Structure editor, 3D modeler and GlycoCT translation:

6. A.Y. Bochkov, Ph.V. Toukach "CSDB/SNFG Structure Editor: an online glycan builder with 2D and 3D structure visualization", J Chem Inf Model, 2021, 61(10): 4940-4948. (PMID 34595926, DOI 10.1021/acs.jcim.1c00917)

   CSDB Linear and comparison of carbohydrate notations:

7. 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. (PMID 31790229, DOI 10.1021/acs.jcim.9b00744)

   SMILES & 3D generation:

8. 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 (PMID 29547883, DOI 10.1093/bioinformatics/bty168)

   NMR-based structure prediction:

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

   Three papers on glycosyltransferase subdatabase:

10. K.S Egorova, Ph.V. Toukach "CSDB_GT : a new curated database on glycosyltransferases", Glycobiology, 2017, 27(4): 285-290. (PMID 28011601, DOI 10.1093/glycob/cww137)
11. K.S Egorova, Yu.A. Knirel, Ph.V. Toukach "Expanding CSDB_GT glycosyltransferase database with Escherichia coli", Glycobiology, 2019, 29(4): 285-287. (PMID 30759212, DOI 10.1093/glycob/cwz006)
12. K.S Egorova, N.S. Smirnova, Ph.V. Toukach "CSDB_GT, a curated glycosyltransferase database with close-to-full coverage on three most studied non-animal species", Glycobiology, 2021, 31(5): 524-529. (PMID 33242091, DOI 10.1093/glycob/cwaa107)

    Glycoepitope subdatabase:

13. Ph.V. Toukach "Supplementing the Carbohydrate Structure Database with glycoepitopes", Glycobiology, 2023, 33(7):528-531. (PMID 37306951, DOI 10.1093/glycob/cwad043)

    Two CSDB overviews:

14. Ph.V. Toukach, K.S Egorova "Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts", Nucleic Acids Res - Database Issue, 2016, 44(D1): D1229-D1236. (PMID 262861940, DOI 10.1093/nar/gkv840)
15. Ph.V. Toukach "Carbohydrate Structure Database: current state and recent developments", Analytical and Bioanalytical Chemistry, 2024. (PMID 38914734, DOI 10.1007/s00216-024-05383-w)

    Three papers on statistical studies of the CSDB content and taxon clustering:

16. 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. (PMID 26337239, DOI 10.1093/database/bav073)
17. Ph.V. Toukach, K.S Egorova "Examining the diversity of structural motifs in fungal glycome", Comput Struct Biotechnol J, 2022, 20:5466-5476. (PMID 36249563, DOI 10.1016/j.csbj.2022.09.040)
18. 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. (PMID 18694500, DOI 10.1186/1472-6807-8-35)

    Two chapters on features and typical scientific challenges solved by CSDB:

19. Ph. Toukach, K. Egorova "Carbohydrate Structure Database (CSDB): examples of usage", in "A Practical Guide to Using Glycomics Databases", ed: K.F. Aoki-Kinoshita. Springer Japan, 2017, ch.5., pp. 75-113. (DOI 10.1007/978-4-431-56454-6_5, online ISBN 978-4-431-56454-6, print ISBN 978-4-431-56452-2)
20. 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 10.1007/978-1-4939-2343-4_5, online ISBN 978-1-4939-2343-4, print ISBN 978-1-4939-2342-7)

    Paper on the ontology for glycomic data exchange:

21. 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. (PMID 25388145, DOI 10.1093/bioinformatics/btu732)

    Three papers on CSDB NMR simulation service:

22. 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 25020143, DOI 10.1021/ci500267u)
23. R.R. Kapaev, Ph.V. Toukach "Improved carbohydrate structure generalization scheme for ¹H and ¹³C NMR simulations.", Anal Chem, 2015, 87: 7006-7010. (PMID 26087011, DOI 10.1021/acs.analchem.5b01413)
24. R.R. Kapaev, Ph.V. Toukach "Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software", J Chem Inf Model, 2016, 56: 1100-1104. (PMID 27227420, DOI 10.1021/acs.jcim.6b00083)

    Chapter on daily usage of CSDB:

25. 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. (DOI 10.1007/978-4-431-54841-6_24, online ISBN 978-4-431-54836-2, print ISBN 978-4-431-54840-9)

    Presentation of Plant&Fungal CSDB:

26. K.S. Egorova, Ph.V. Toukach "Expansion of coverage of Carbohydrate Structure Database (CSDB)", Carbohydr Res, 2013, 389: 112-114. (PMID 24680503, DOI 10.1016/j.carres.2013.10.009)

    Two papers on cross-database integration in glycomics:

27. K.F. Aoki-Kinoshita et al. "The fifth ACGG-DB meeting report: Towards an international glycan structure repository", Glycobiology 2013, 23: 1422-1424. (PMID 24190976, DOI 10.1093/glycob/cwt084)
28. 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 24280648, DOI 10.1186/2041-1480-4-39)

    Mini-review on existing carbohydrate databases:

29. Ph.V. Toukach "CSDB and other carbohydrate databases", Glycoconjugate J, 2013, 30: 347-349.

    Two papers on data quality in glycan databases:

30. K.S. Egorova, Ph.V. Toukach "Critical analysis of CCSD data quality", J Chem Inf Model, 2012, 52: 2812-2814. (PMID 23025661, DOI 10.1021/ci3002815)
31. K.V. Kazantsev, Ph.V. Toukach "Remediation of the NMR data of natural glycans", Int J Biol Macromol, 2024, 137042 . (PMID 39521218, DOI 10.1016/j.ijbiomac.2024.137042)

    Paper on CSDB ideology, control programs, interface and comparison of existing databases:

32. Ph. Toukach "Bacterial Carbohydrate Structure Database 3: principles and realization", J Chem Inf Model 2011, 51(1): 159-170. (PMID 21155523, DOI 10.1021/ci100150d)

    First journal publication on the interaction between glyco-databases:

33. 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. (PMID 17202164, DOI 10.1093/nar/gkl883)

    First presentation of bacterial CSDB:

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

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