Introducing glycomics data into the Semantic Web | Sciact - научная деятельность

Introducing glycomics data into the Semantic Web Научная публикация

Журнал

Journal of Biomedical Semantics
ISSN: 2041-1480

Вых. Данные

Год: 2013, Том: 4, Номер: 1, Номер статьи : 39, Страниц : DOI: 10.1186/2041-1480-4-39

Авторы

Aoki-Kinoshita Kiyoko F ¹ , Bolleman Jerven ² , Campbell Matthew P ³ , Kawano Shin ⁴ , Kim Jin-Dong ⁴ , Lütteke Thomas ⁵ , Matsubara Masaaki ⁶ , Okuda Shujiro ⁷ , Ranzinger Rene ⁸ , Sawaki Hiromichi ⁹ , Shikanai Toshihide ⁹ , Shinmachi Daisuke ⁹ , Suzuki Yoshinori ⁹ , Toukach Philip ¹⁰ , Yamada Issaku ⁶ , Packer Nicolle H ³ , Narimatsu Hisashi ⁹

Организации

1	Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577, Japan
2	Swiss Institute of Bioinformatics, CMU 1, rue Michel Servet 1211, Geneva, Switzerland
3	Biomolecular Frontiers Research Centre, Macquarie University, Sydney, New South Wales, Australia
4	Database Center for Life Science, Research Organization of Information and Systems, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
5	Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Frankfurter Str. 100, 35392, Giessen, Germany
6	Laboratory of Glyco-organic Chemistry, The Noguchi Institute, 1-8-1 Kaga, Itabashi-ku, Tokyo, 173-0003, Japan
7	Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
8	Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30602, USA
9	Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba Central-2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
10	NMR Laboratory, N.D. Zelinsky Institute of Organic Chemistry, Leninsky prospekt 47, 119991, Moscow, Russia

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.

Aoki-Kinoshita K.F. , Bolleman J. , Campbell M.P. , Kawano S. , Kim J-D. , Lütteke T. , Matsubara M. , Okuda S. , Ranzinger R. , Sawaki H. , Shikanai T. , Shinmachi D. , Suzuki Y. , Toukach P. , Yamada I. , Packer N.H. , Narimatsu H.
Introducing glycomics data into the Semantic Web
Journal of Biomedical Semantics. 2013. V.4. N1. 39 . DOI: 10.1186/2041-1480-4-39 WOS Scopus OpenAlex

≡ Web of science:	WOS:000343706500007
≡ Scopus:	2-s2.0-84904731418
≡ OpenAlex:	W2152669438