Introducing glycomics data into the Semantic Web

Kiyoko F. Aoki-Kinoshita, Jerven Bolleman, Matthew P. Campbell, Shin Kawano, Jin Dong Kim, Thomas Lütteke, Masaaki Matsubara, Shujiro Okuda, Rene Ranzinger, Hiromichi Sawaki, Toshihide Shikanai, Daisuke Shinmachi, Yoshinori Suzuki, Philip Toukach, Issaku Yamada, Nicolle H. Packer, Hisashi Narimatsu*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

33 Citations (Scopus)

Abstract

Background: Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as "switches" that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases. Results: In order to implement support for the Semantic Web most efficiently for glycomics research, the developers of major glycomics databases agreed on a minimal standard for representing glycan structure and annotation information using RDF (Resource Description Framework). Moreover, all of the participants implemented this standard prototype and generated preliminary RDF versions of their data. To test the utility of the converted data, all of the data sets were uploaded into a Virtuoso triple store, and several SPARQL queries were tested as "proofs-of-concept" to illustrate the utility of the Semantic Web in querying across databases which were originally difficult to implement. Conclusions: We were able to successfully retrieve information by linking UniCarbKB, GlycomeDB and JCGGDB in a single SPARQL query to obtain our target information. We also tested queries linking UniProt with GlycoEpitope as well as lectin data with GlycomeDB through PDB. As a result, we have been able to link proteomics data with glycomics data through the implementation of Semantic Web technologies, allowing for more flexible queries across these domains.

Original languageEnglish
Article number39
Pages (from-to)1-7
Number of pages7
JournalJournal of Biomedical Semantics
Volume4
DOIs
Publication statusPublished - 26 Nov 2013

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