title: Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Masashi
authors.initials: M
authors.lastname: Yokochi
authors.affiliation: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Naohiro
authors.initials: N
authors.lastname: Kobayashi
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
authors.forename: Eldon L
authors.initials: EL
authors.lastname: Ulrich
authors.affiliation: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Akira R
authors.initials: AR
authors.lastname: Kinjo
authors.affiliation: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Iwata
authors.affiliation: Department of Informatics & Telecommunications, University of Athens, Athens, Greece.
authors.forename: Yannis E
authors.initials: YE
authors.lastname: Ioannidis
authors.affiliation: Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.
authors.forename: Miron
authors.initials: M
authors.lastname: Livny
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
authors.forename: John L
authors.initials: JL
authors.lastname: Markley
authors.affiliation: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Haruki
authors.initials: H
authors.lastname: Nakamura
authors.affiliation: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Chojiro
authors.initials: C
authors.lastname: Kojima
authors.affiliation: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan. tfjwr@protein.osaka-u.ac.jp.
authors.forename: Toshimichi
authors.initials: T
authors.lastname: Fujiwara
mesh_terms: D064229:Biological Ontologies; D030562:Databases, Protein; D020407:Internet; D019906:Nuclear Magnetic Resonance, Biomolecular; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012660:Semantics
chemical_list: D011506:Proteins
keywords: BMRB; Database; NMR; RDF; XML