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Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.

Authors :
Masashi Yokochi
Naohiro Kobayashi
Ulrich, Eldon L.
Akira R. Kinjo
Takeshi Iwata
Yannis E. Ioannidis
Livny, Miron
Markley, John L.
Haruki Nakamura
Chojiro Kojima
Toshimichi Fujiwara
Source :
Journal of Biomedical Semantics; 5/5/2016, Vol. 7, p1-4, 4p
Publication Year :
2016

Abstract

Background: The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases. Findings: To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data. Moreover, a SPARQL endpoint has been deployed. The described case study demonstrates that a simple query of the SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used in NMR and structure-based analysis of proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes. Conclusions: We have developed BMRB/XML and BMRB/RDF and demonstrate their use in performing a federated SPARQL query linking the BMRB to other databases through standard semantic web technologies. This will facilitate data exchange across diverse information resources. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
20411480
Volume :
7
Database :
Complementary Index
Journal :
Journal of Biomedical Semantics
Publication Type :
Academic Journal
Accession number :
115416102
Full Text :
https://doi.org/10.1186/s13326-016-0057-1