GlycoRDF: An ontology to standardize glycomics data in RDF

Rene Ranzinger; Kiyoko F. Aoki-Kinoshita; Matthew P. Campbell; Shin Kawano; Thomas Lütteke; Shujiro Okuda; Daisuke Shinmachi; Toshihide Shikanai; Hiromichi Sawaki; Philip Toukach; Masaaki Matsubara; Issaku Yamada; Hisashi Narimatsu

doi:10.1093/bioinformatics/btu732

GlycoRDF: An ontology to standardize glycomics data in RDF

Rene Ranzinger^*, Kiyoko F. Aoki-Kinoshita, Matthew P. Campbell, Shin Kawano, Thomas Lütteke, Shujiro Okuda, Daisuke Shinmachi, Toshihide Shikanai, Hiromichi Sawaki, Philip Toukach, Masaaki Matsubara, Issaku Yamada, Hisashi Narimatsu

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

35 Citations (Scopus)

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/).

Original language	English
Pages (from-to)	919-925
Number of pages	7
Journal	Bioinformatics
Volume	31
Issue number	6
DOIs	https://doi.org/10.1093/bioinformatics/btu732
Publication status	Published - 15 Mar 2015

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title = "GlycoRDF: An ontology to standardize glycomics data in RDF",

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/).",

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AU - Aoki-Kinoshita, Kiyoko F.

AU - Campbell, Matthew P.

AU - Kawano, Shin

AU - Lütteke, Thomas

AU - Okuda, Shujiro

AU - Shinmachi, Daisuke

AU - Shikanai, Toshihide

AU - Sawaki, Hiromichi

AU - Toukach, Philip

AU - Matsubara, Masaaki

AU - Yamada, Issaku

AU - Narimatsu, Hisashi

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GlycoRDF: An ontology to standardize glycomics data in RDF

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