Database Commons

a catalog of worldwide biological databases

Over the last two decades, several carbohydrate structure databases have been developed and made publicly available by different research groups around the world. This led to the fragmentation of information about carbohydrate structures into different resources that have no or only weak interaction with each other. GlycomeDB was developed to integrate the carbohydrate structures from different resources by generating a single-indexed catalog of these structures that associates each structure with its reference in the original resources. GlycomeDB facilitates searching for carbohydrate structures in all the integrated resources by eliminating the need to use several different search interfaces and manually integrating the results. References provided by GlycomeDB make it possible to retrieve information that is beyond the scope of GlycomeDB but present in the integrated databases. This chapter illustrates the use of the GlycomeDB search interfaces and web services by way of three example cases.

GlycomeDB integrates the structural and taxonomic data of all major public carbohydrate databases, as well as carbohydrates contained in the Protein Data Bank, which renders the database currently the most comprehensive and unified resource for carbohydrate structures worldwide. GlycomeDB retains the links to the original databases and is updated at weekly intervals with the newest structures available from the source databases. The complete database can be downloaded freely or accessed through a Web-interface (www.glycome-db.org) that provides flexible and powerful search functionalities.

Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource.