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Bioinformatics. 2015 Mar 15;31(6):919-25. doi: 10.1093/bioinformatics/btu732. Epub 2014 Nov 11.

GlycoRDF: an ontology to standardize glycomics data in RDF.

Author information

1
Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.
2
Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco-organic Chemistry, The Noguchi Institute, Tokyo, Japan.

Abstract

MOTIVATION:

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.

RESULTS:

An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (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 are available online (http://www.glycoinfo.org/GlycoRDF/).

PMID:
25388145
PMCID:
PMC4380026
DOI:
10.1093/bioinformatics/btu732
[Indexed for MEDLINE]
Free PMC Article

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