Bacterial, plant, and fungal carbohydrate structure databases: daily usage

Area of Science:

• Glycoscience
• Bioinformatics
• Carbohydrate Chemistry

Background:

• Natural carbohydrates are crucial in biological systems, serving as diagnostic and therapeutic targets.
• Glycomics aims to systematize carbohydrate information and understand their roles in human health and disease.
• Existing databases and computational tools are insufficient for navigating the rapidly growing glycomic information landscape.

Purpose of the Study:

• To introduce the Bacterial Carbohydrate Structure Database (CSDB) as a solution for organizing and accessing carbohydrate structure information.
• To highlight the features and utility of CSDB for scientific practice in glycomics.
• To encourage the use of CSDB for research on bacterial, archaeal, plant, and fungal carbohydrates.

Main Methods:

• Development of the Bacterial Carbohydrate Structure Database (CSDB).
• Inclusion of structural, bibliographic, taxonomic, and NMR spectroscopic data for carbohydrates.
• Expansion of CSDB to include plant and fungal carbohydrate structures.
• Ensuring high data consistency and manual verification of annotations.

Main Results:

• CSDB offers over 90% coverage of bacterial and archaeal carbohydrate structures.
• Data consistency in CSDB exceeds 90%, with error-free records.
• CSDB provides manually verified bibliographic, NMR spectroscopic, and taxonomic annotations.
• The database has been expanded to encompass plant and fungal carbohydrate data.

Conclusions:

• CSDB is a valuable, freely available web service essential for glycomics research.
• The database facilitates orientation within the complex glycomic information space.
• Continued expansion of CSDB is expected to achieve full coverage across various biological domains.