RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data

Abstract Background The abundance of glycomics data that have accumulated has led to the development of many useful databases to aid in the understanding of the function of the glycans and their impact on cellular activity. At the same time, the endeavor for data sharing between glycomics databases with other biological databases have contributed to the creation of new knowledgebases. However, different data types in data description have impeded the data sharing for knowledge integration. To solve this matter, Semantic Web techniques including Resource Description Framework (RDF) and ontology development have been adopted by various groups to standardize the format for data exchange. These semantic data have contributed to the expansion of knowledgebases and hold promises of providing data that can be intelligently processed. On the other hand, bench biologists who are experts in experimental finding are end users and data producers. Therefore, it is indispensable to reduce the technical barrier required for bench biologists to manipulate their experimental data to be compatible with standard formats for data sharing.