R. Ranzinger1, K.F. Aoki-Kinoshita2,3, M.P. Campbell4, S. Kawano5, T. Lütteke6, S. Okuda7, D. Shinmachi3, T. Shikanai2, H. Sawaki2, Ph.V. Toukach8, M. Matsubara9, I. Yamada9, H. Narimatsu2
1Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
2Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
3Department of Bioinformatics, Faculty of Engineering, Soka University, Tokyo, Japan
4Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia
5Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan
6Institute of Veterinary Physiology and Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
7Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
8Zelinsky Institute of Organic Chemistry, Moscow, Russia 9Laboratory of Glycoorganic Chemistry, The Noguchi Institute, Tokyo, Japan
KEYWORDS: Resource Description Framework, Glycomics, Ontology, Data integration
Bioinformatics, 2015, v.31(6), pp. 919-925
DOI: 10.1093/bioinformatics/btu732, PMID: 25388145
Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information.
An international group of bioinformatics experts in the field of glycomics have worked together to create a standard RDF representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine readable exports of the data stored in their databases.
Availability and Implementation
The ontology, supporting documentation and source code used by database providers to generate standardized RDF can be accessed from http://www.glycoinfo.org/GlycoRDF/