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- Title
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
- 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.
- Subjects
NUCLEAR magnetic resonance spectroscopy; MACROMOLECULES; RELATIONAL databases
- Publication
Journal of Biomedical Semantics, 2016, Vol 7, p1
- ISSN
2041-1480
- Publication type
Article
- DOI
10.1186/s13326-016-0057-1