Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins

Journal of Biomedical Semantics

Volumn 7, Issue 1, 2016, Pages

  Yokochi, Masashi ^a   Kobayashi, Naohiro ^a   Ulrich, Eldon L ^b   Kinjo, Akira R ^a   Iwata, Takeshi ^a   Ioannidis, Yannis E ^c   Livny, Miron ^d   Markley, John L ^b   Nakamura, Haruki ^a   Kojima, Chojiro ^a   Fujiwara, Toshimichi ^a  

^a OSAKA UNIVERSITY   (Japan)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c UNIVERSITY OF ATHENS   (Greece)

^d University of Wisconsin Madison   (United States)

Author keywords

BMRB; Database; NMR; RDF; XML

Indexed keywords

PROTEIN;

BIOLOGICAL ONTOLOGY; CHEMISTRY; INTERNET; METABOLISM; NUCLEAR MAGNETIC RESONANCE; PROTEIN DATABASE; SEMANTICS;

BIOLOGICAL ONTOLOGIES; DATABASES, PROTEIN; INTERNET; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS; SEMANTICS;

EID: 84965005779     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/s13326-016-0057-1     Document Type: Article

References (18)

1. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL. BioMagResBank. Nucleic Acids Res. 2008;36:D402-8.
2. Hall SR. The STAR File: a new format for electronic data transfer and archiving. J Chem Inf Comput Sci. 1991;31:326-33.
3. Hall SR, Spadaccini N. The STAR File: Detailed Specifications. J Chem Inf Comput Sci. 1994;34:505-8.
4. Spadaccini N, Hall SR. Extensions to the STAR File Syntax. J Chem Inf Model. 2012;52(8):1901-6.
5. Wang L, Eghbalnia HR, Bahrami A, Markley JL. Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications. J Biomol NMR. 2005;32:13-22.
6. Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL. PACSY, a relational database management system for protein structure and chemical shift analysis. J Biomol NMR. 2012;54:169-79.
7. Joseph AP, Agarwal G, Mahajan S, Gelly JC, Swapna LS, Offmann B, Cadet F, Bornot A, Tyagi M, Valadié H, Schneider B, Etchebest C, Srinivasan N, De Brevern AG. A short survey on protein blocks. Biophys Rev. 2010;2:137-47.
8. XML Schema Definition Language (XSD) 1.1 Part 1: Structures. 2012, http://www.w3.org/TR/xmlschema11-1/. Accessed 27 October 2015.
9. XSL Transformation (XSLT) Version 2.0. 2007, http://www.w3.org/TR/xslt20/. Accessed 27 October 2015.
10. RDF Schema 1.1. 2014, http://www.w3.org/TR/rdf-schema/. Accessed 27 October 2015.
11. OWL 2 Web Ontology Language Document Overview (Second Edition). 2012, http://www.w3.org/TR/owl2-overview/. Accessed 27 October 2015.
12. Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudou T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H. Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res. 2012;40:D453-60.
13. Berners-Lee T. Linked Data, In Design Issues: Architectural and Philosophical Points. 2006, http://www.w3.org/DesignIssues/LinkedData. Accessed 27 October 2015.
14. Juty N, Le Novère N, Laibe C. Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res. 2012;40:D580-6.
15. Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J. Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. J Biomed Inform. 2008;41:706-16.
16. SPARQL 1.1 Query Language. 2013, http://www.w3.org/TR/sparql11-query/. Accessed 27 Oct 2015.
17. DuCharme B. Learning SPARQL. Sebastopol: O'Reilly Media, Inc.; 2011; ISBN: 978-1-449-30659-5.
18. Wakefield RI, Smith BO, Nan X, Free A, Soteriou A, Uhrin D, Bird AP, Barlow PN. The solution structure of the domain from MeCP2 that binds to methylated DNA. J Mol Biol. 1999;291:1055-65.