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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.
SUBMITTER: Yokochi M
PROVIDER: S-EPMC5143449 | biostudies-literature | 2016 May
REPOSITORIES: biostudies-literature
Yokochi Masashi M Kobayashi Naohiro N Ulrich Eldon L EL Kinjo Akira R AR Iwata Takeshi T Ioannidis Yannis E YE Livny Miron M Markley John L JL Nakamura Haruki H Kojima Chojiro C Fujiwara Toshimichi T
Journal of biomedical semantics 20160505 1
<h4>Background</h4>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.<h4>Findings</h4> ...[more]