BCSDB, a database containing data on bacterial carbohydrates with known primary structure, has been developed. The key points in this project are coverage, consistency and automated operations.
Currently, the BCSDB contains about 9000 records on bacterial carbohydrates, including the corresponding part of CarbBank, a biggest carbohydrate database developed in the end of XXth century (about 3000 records on bacterial structures published before 1995). Th? BCSDB coverage is approaching the total number of bacterial carbohydrate structures reported until 2007. The expected growth is ~400 structures per year.
Data from both literature and CarbBank have been checked for consistency prior to the upload and corrected when necessary. Comparison of the consistency of free carbohydrate databases showed the outstanding data intregrity in BCSDB.
The BCSDB interface includes the web-based user part, web-based administrator part and programming gateways for automated data interchange (cross-referring to other databases containing information on natural carbohydrates). Currently it is cross-linked with NCBI PubMed, NCBI Taxonomy and GlycoSCIENCES.de. The BCSDB is available at http://www.glyco.ac.ru/bcsdb/ for free usage and validated user data submission.
In addition to the structure and bibliography, each record in the CSDB contains the abstract of the publication, data on the carbohydrate source, methods of structure elucidation, information on the availability of spectral data and assignment of NMR spectra when available, data on conformation, biological activity, chemical and enzymatic synthesis, biosynthesis, genetics and other related data. The search may be performed using a fragment(s) of structure or NMR spectra, or indexed tags, including carbohydrate source, keywords and bibliography.
BCSBD was developed within the framework of the International Science and Technology Center Partner Project, supported by the Cooperative Threat Reduction Program of the US Department of Defense (ISTC Partner). The further funding originated from Russian Foundation of Basic Research and Russian Federation President grant committee. My role in this project were general engineering, database architecture, data format, structure encoding language, web-design, scripting (partially), coordination of database filling and cross-database interfaces.
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Download an electronic presentation of BCSDB, as used on dedicated workshop in 2005 Jul 12-14, Moscow (ZIPped MS PowerPoint-2000 document, 224 Kb) |
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