Ranzinger Rene, Aoki-Kinoshita Kiyoko F, Campbell Matthew P, Kawano Shin, Lütteke Thomas, Okuda Shujiro, Shinmachi Daisuke, Shikanai Toshihide, Sawaki Hiromichi, Toukach Philip, Matsubara Masaaki, Yamada Issaku, Narimatsu Hisashi
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 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.
Bioinformatics. 2015 Mar 15;31(6):919-25. doi: 10.1093/bioinformatics/btu732. Epub 2014 Nov 11.
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 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.
The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/).
在过去几十年中,已经创建了几个基于糖组学的生物信息学资源和数据库并向公众发布。不幸的是,在存储信息的表示方面没有通用标准,也没有一个通用的机器可读接口,使得生物信息学团队能够轻松提取和交叉引用存储的信息。
糖组学领域的一个国际生物信息学专家小组共同努力,为糖组学数据创建了一个标准的资源描述框架(RDF)表示,重点是聚糖序列以及相关的生物来源、出版物和实验数据。这个RDF标准由GlycoRDF本体定义,数据库提供者将使用它来生成其数据库中存储数据的通用机器可读导出。
数据库提供者用于生成标准化RDF的本体、支持文档和源代码可在线获取(http://www.glycoinfo.org/GlycoRDF/)。