CSDB: credits

The CSDB team is/was:
Philip Toukach, Assoc. Prof. Bacterial, Plant&Fungal:
management, research&development,
programming, data verification
Yuriy Knirel, Prof. Bacterial: management, data verification
Plant&Fungal: general support

Ksenia Egorova, PhD Bacterial, Plant&Fungal:
manual literature processing,
data verification

Nadezhda Kalinchuk, PhD Bacterial, Plant&Fungal:
manual literature processing,
data annotation and posting
 
Mikhail Dolgov
Roman Kapaev
NMR tools: programming
  Stella Khalfina
Evelina Zdorovenko, PhD
Andrey Perepelov, PhD
Anna Kondakova, PhD
Olga Ovchinnikova, PhD
N. Chekareva, PhD
Bacterial: data posting
  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
Pilot project: workshop organisation
  Pavel Belyakov, PhD † Bacterial: server administration
  Claus-Willi von der Lieth, Prof. †
Thomas Lütteke, Prof.
Stephan Herget, PhD
Rene Ranzinger
colsultations and critics
currently active members
Acknowledgements

The first version of Bacterial CSDB (CSBD-II) 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) and N15-04-01065 (2015-2017), 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 third pack originates from our own curation efforts on publications selected from the NCBI Pubmed and Thomson Reuters Web Of Science databases.

The Bacterial (BCSDB) and Plant&Fungal (PFCSDB) databases were joined in 2015 to improve the quality of content-dependent services, such as taxon clustering or NMR simulation. The separate databases will be supported in parallel until 2018.

Citing and feedback

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

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

 

Publications

    Glycosyltransferase subdatabase:

  1. 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)

    Overview of the merged CSDB:

  2. 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)

    Statistical studies of CSDB content and taxon clustering:

  3. 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)

    Chapter on typical scientific tasks solved by CSDB:

  4. 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:

  5. 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 prediction service:

  6. 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)
  7. 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)
  8. 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:

  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. (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:

  10. 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:

  11. 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)
  12. 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:

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

    Paper on Carbbank data validation within CSDB:

  14. 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)

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

  15. 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)

    Paper on comparative analysis of Bacterial CSDB content:

  16. 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)

    First journal publication in English dedicated to cross-database interaction:

  17. 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:

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


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