PAConto: RDF Representation of PACDB Data and Ontology of Infectious Diseases Known to Be Related to Glycan Binding

Abstract

The Pathogen Adherence to Carbohydrate Database (PACDB) has been developed by the Research Center for Medical Glycoscience (RCMG) and released in March 2010. Being the members of the “Life-Science Database Integration Project” of National Bioscience Database Center (NBDC) of Japan Science and Technology Agency (JST), we have decided to organize PACDB information and enrich its content by integration with other biomedical resources. We have designed and developed the ontology, called PAConto. This ontology is based on the Semantic Web technologies and is represented in Resource Description Framework (RDF) format. Using the Semantic Web approach with Web Ontology Language (OWL), Simple Knowledge Organization System (SKOS), and RDF standards, we have described the semantics of PACDB data, enriched this data with additional various classifications, and linked PACDB data with related biomedical resources. In addition to the ontology, we have developed a system with a user interface, using which the users can retrieve and search information from PAConto. The RDF files for PAConto with RDF/SPARQL-based user interface, documentation, and user’s guide are available at http://acgg.asia/db/diseases/. In this chapter, we will introduce the topics of PACDB and PAConto and explain how the users can navigate through this system and search and display RDF data. Also, we will provide the contact information for feedback purposes. We hope that this PAConto ontology with PACDB database will help the users to better understand the etiology, pathogenesis, and manifestations of the diseases known to be related to glycan binding.