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Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.
- 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]
- Subjects :
- NUCLEAR magnetic resonance spectroscopy
MACROMOLECULES
RELATIONAL databases
Subjects
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