Glyco-Disease Genes Database (GDGDB) and Pathogen Adherence to Carbohydrate Database (PACDB) have been developed by the Research Center for Medical Glycoscience. With the purpose to organize their information and enrich their contents with data from other biomedical resources we have designed and created GDGDB RDF & GGDonto ontology and PAConto ontology, respectively. These ontologies are based on the Semantic Web technologies and represented in RDF. We hope that these ontologies and databases will help the users to better understand the etiology, pathogenesis and manifestations of the diseases known to be related to glycan metabolism and glycan binding.