Τίτλος:
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins
Γλώσσες Τεκμηρίου:
Αγγλικά
Περίληψη:
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. © 2016 Yokochi et al.
Συγγραφείς:
Yokochi, M.
Kobayashi, N.
Ulrich, E.L.
Kinjo, A.R.
Iwata, T.
Ioannidis, Y.E.
Livny, M.
Markley, J.L.
Nakamura, H.
Kojima, C.
Fujiwara, T.
Περιοδικό:
Journal of Biomedical Semantics
Εκδότης:
BioMed Central Ltd.
Λέξεις-κλειδιά:
protein, biological ontology; chemistry; Internet; metabolism; nuclear magnetic resonance; protein database; semantics, Biological Ontologies; Databases, Protein; Internet; Nuclear Magnetic Resonance, Biomolecular; Proteins; Semantics
DOI:
10.1186/s13326-016-0057-1
