./js/glycomedb.js ./css/glycomedb.css carbohydrate,carbohydrate structures Rene Ranzinger

Carbohydrates are the third major class of biological macromolecules, besides proteins and DNA molecules. They are involved in numerous biological processes, among them protein folding and inter/intra cell recognition. In contrast to DNA and proteins neither a comprehensive database for carbohydrate structures nor a universal nomenclature for computational purposes exists. After the cease of funding for the Complex Carbohydrate Structure Database (CCSDB, often referred as CarbBank) in 1997, four initiatives developed independent databases with partially overlapping foci. For each database, a proprietary encoding scheme for residues and topology of the structures was designed. As a result it is virtually impossible to get an overview of all existing structures, and to compare the contents of the different databases. We have analysed all of the existing public databases and defined a sequence format based on XML (GlycoCT) capable of storing all structural information of carbohydrate sequences. We have implemented a library of parsers for the interpretation of the different encoding schemes for carbohydrates. With this library we have translated the carbohydrate sequences of all freely available databases (CFG , KEGG, GLYCOSCIENCES.de, BCSDB and Carbbank) to GlycoCT, and created a new database (GlycomeDB) containing all structures and annotations. During the process of data integration we found multiple inconsistencies in the existing databases which were corrected in collaboration with the responsible curators. With the new database, GlycomeDB, it is possible to get an overview of all carbohydrate structures in the different databases and to crosslink common structures in the different databases. Scientists are now able to search for a particular structure in the meta database and get information about the occurrence of this structure in the five carbohydrate structure databases. Presentation of GlycomeDB at the Glycobiology meeting in Boston. Adding ID search in the database section. Presentation of GlycomeDB at the EUROCARB14 in Lübeck. Presentation of GlycomeDB at the Glycobioinformatics and Modeling Workshop in Heidelberg. First version of the webinterface of GlycomeDB online. GlycomeDB project starts. First of all, we have to thank Dr. Claus-Wihelm von der Lieth, who was our group leader at the German Cancer Research Center in Heidelberg. We will not forget his devotion to the scientific work and his restless dedication to the development of glycomics resources. He gave us the possibility to pursue the effort of creating a unified database and provided us with ideas and contacts to our collaborators, which made this project possible. We also thank the German Research Foundation and the Sixth Framework Programme of the Europian Union for funding. We want to thank all the carbohydrate databases initiatives ( , CarbBank, and ), which allowed open access to their data and made this project successful and useful for the carbohydrate community. We would like to thank Alessio Ceroni, who has developed the Java applet that allows for simple and intuitive structure input. We used the library of , which was also developed by Alessio, for the generation of all carbohydrate structure images on our pages. In addition we want to thank all our colleagues in the which helped us with a lot of fruitful discussions and comments. Last but not least, we wish to thank all open source and open access Java projects. This webpage would be unthinkable without JDOM, Webworks and many other libraries.