2016年5月
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins
JOURNAL OF BIOMEDICAL SEMANTICS
- 巻
- 7
- 号
- 1
- 開始ページ
- 16
- 終了ページ
- 記述言語
- 英語
- 掲載種別
- 研究論文(学術雑誌)
- DOI
- 10.1186/s13326-016-0057-1
- 出版者・発行元
- BIOMED CENTRAL LTD
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.
- リンク情報
- ID情報
-
- DOI : 10.1186/s13326-016-0057-1
- ISSN : 2041-1480
- PubMed ID : 27927232
- Web of Science ID : WOS:000375703100001