AP Joseph

AR Kinjo

EL Ulrich

F Belleau

L Wang

N Juty

N Spadaccini

RI Wakefield

SR Hall

W Lee

Journal of Biomedical Semantics

English

Masashi Yokochi

Naohiro Kobayashi

Eldon L. Ulrich

Akira R. Kinjo

Takeshi Iwata

Yannis E. Ioannidis

Miron Livny

John L. Markley

Haruki Nakamura

Chojiro Kojima

Toshimichi Fujiwara

Crossref

SHORT REPORT Open AccessPublication of nuclear magnetic resonanceexperimental data with semantic webtechnology and the application thereof tobiomedical research of proteinsMasashi Yokochi1, Naohiro Kobayashi1, Eldon L. Ulrich2, Akira R. Kinjo1, Takeshi Iwata1, Yannis E. Ioannidis3,Miron Livny4, John L. Markley2, Haruki Nakamura1, Chojiro Kojima1 and Toshimichi Fujiwara1*AbstractBackground: The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived atthe BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR dataarchived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairlydifficult for users to retrieve data from the NMR-STAR files or the relational database in association with data fromother biological databases.Findings: To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries totwo 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 ofthe SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used inNMR 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 federatedSPARQL query linking the BMRB to other databases through standard semantic web technologies. This will facilitatedata exchange across diverse information resources.Keywords: NMR, BMRB, Database, XML, RDFFindingsBackgroundThe BioMagResBank (BMRB; http://www.bmrb.wisc.edu/)is a worldwide data repository for experimental and de-rived data gathered from nuclear magnetic resonance(NMR) spectroscopic studies of biological molecules [1].For more than 15 years, the BMRB has used and devel-oped the NMR-STAR format based on the STAR formatspecifications [2–4] for data archiving and data exchange(see Fig. 1a). The NMR-STAR Dictionary, acting as ontol-ogy for NMR-STAR data, continues to be improved andexpanded to keep up with the needs of the biomolecularNMR community. The most important parameterarchived in the BMRB is assigned chemical shifts, whichcan be used directly to determine protein secondary struc-ture and to assist in the determination of their solutionstructures, to identify interactions of small molecules withtarget proteins for drug discovery, and to characterizeprotein-protein interactions.As of 2015, the BMRB archive contains more than10,000 entries, and ~800 new entries are being addedeach year. This growing biological data archive hasraised researchers’ interest in integrating the diversebiological information resources to form new hypothesesfor understanding biological functions and phenomena.The best approach for enhancing interoperability of the* Correspondence: tfjwr@protein.osaka-u.ac.jp1Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka565-0871, JapanFull list of author information is available at the end of the article© 2016 Yokochi et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, andreproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link tothe Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Yokochi et al. Journal of Biomedical Semantics  (2016) 7:16 DOI 10.1186/s13326-016-0057-1Fig. 1 The sequential data conversion of a BMRB entry from NMR-STAR format. a Part of a BMRB entry in NMR-STAR format. Parts of the entryhave been converted to b XML format and c RDF format. d Schematic representation of linked external information resources, where shorter distancesfrom the BMRB represent closer relationships with the BMRBYokochi et al. Journal of Biomedical Semantics  (2016) 7:16 Page 2 of 4BMRB would be to convert the archive into standardweb formats, XML and RDF, using a data structure thatcorresponds closely to the NMR-STAR ontologydescribed by an XML schema and OWL.MethodsWe have extended the NMR-STAR Dictionary to accom-modate the derived data repositories on BMRB, such asLACS validation reports [5], structural annotations usingPACSY [6] and Protein Blocks [7], etc., followed by transla-tion of the dictionary to an XML schema [8] (BMRB/XMLSchema), using the PDBx/mmCIF Dictionary Suite de-veloped by the Research Collaboratory for StructuralBioinformatics (RCSB) Protein Data Bank (PDB)(http://sw-tools.rcsb.org/). To automate the XML con-version of BMRB entries, we have developed a softwaresuite (the BMRBxTool) that generates XML documentsand validates their format and data consistency accordingto the BMRB/XML schema. EXtensible Stylesheet Lan-guage (XSL) transformation [9] was applied to generateBMRB entries in RDF format from the corresponding XMLdocuments. Along with the RDF, we also provide itsontology written in RDF/RDFS/OWL syntax as BMRB/OWL [10, 11], which is a direct translation of the BMRB/XML schema. To bridge different data models between theXML tree and the RDF directed graph, we have introducedabstract OWL classes and RDF properties to the ontology[12]. For the data conversion from XML to RDF in accord-ance with the principles of Linked Data [13] and recom-mendations widely accepted by biological databasecommunity [14], we have developed a software suite calledBMRBoTool. We have tested as many as thirty SPARQLqueries to show how NMR experimental data can be re-trieved. In a case study to demonstrate a federated SPARQLquery, we performed a search for phenotypes annotatedwith information for SNPs from the human genome by in-tegrating three SPARQL endpoints: the BMRB, UniProt,and OMIM [see Additional file 1 for details].Results and discussionOn our portal site (http://bmrbpub.protein.osaka-u.ac.jp/,hereafter abbreviated as ‘~/’), we have archived theBMRB/XML (~/archive/xml/), as shown in Fig. 1b. TheBMRB/RDF derived from the reduced version of theFig. 2 Federated search using multiple SPARQL endpoints of the BMRB, UniProt, and OMIM. a An example of a SPARQL query begins from theBMRB entry. b Results performed by the SPARQL query for BMRB entry 4280, showing the BMRB ID, mutation, OMIM ID, dbSNP ID, secondary structure,and SASA. c Ribbon models of NMR structure (PDB: 1QK9) of MECP2. The side-chains (space-filling model) for the mutation (E137 and A140) exposedto solvent are responsible for X-linked mental retardation [18]Yokochi et al. Journal of Biomedical Semantics  (2016) 7:16 Page 3 of 4BMRB/XML (lacking bulky information such as atomiccoordinates and NMR restraints) has also been archived(~/archive/rdf/) as shown in Fig. 1c. A bulk download ser-vice is available using the rsync protocol that helps usersmirror the latest data collections, which are updated peri-odically. A schematic RDF graph of linked databases is il-lustrated in Fig. 1d. Owing to the machine readability ofthe XML format, the BMRB/XML provides users with anexcellent starting point to develop new tools for use inbiochemistry and structural biology. The BMRB/RDF andassociated web services enable the integration of theBMRB archive with other biological databases, which mayfacilitate flexible data exchange and knowledge discovery.Furthermore, we provide a SPARQL endpoint for query-ing the BMRB/RDF (~/search/rdf) in the same way asBio2RDF [15] does. The RDF query language, SPARQL[16], realizes data exchange between databases in a con-cise syntax. The key feature of SPARQL is its capability ofjoining remote SPARQL endpoints in what is called a fed-erated SPARQL query [17]. We confirmed the feasibilityof such a query (see Fig. 2a), by demonstrating search andclassification of SNPs in an associated BMRB entry. In thecase study, we successfully collected residues in a BMRBentry whose sequences correspond to SNPs annotated byOMIM, as shown in Fig. 2b. The search results (Fig. 2c)were represented by structural parameters archived in theBMRB [see also Additional file 1 for methods applied andall results, chapter 3], allowing users to infer biologicalrelationships between the phenotype annotated SNPs andstructural features in human proteins (see Fig. 2c). The re-sults show that the BMRB/RDF offers a promising ap-proach for integrating biophysical information derivedfrom biological NMR spectroscopy with other bioinfor-matics resources of interest in biological and medicalscience research.Additional fileAdditional file 1: Further detail of the BMRB/XML, BMRB/RDF and webservices including SPARQL endpoint. Complete results of the SPARQLquery (Fig. 2a) and many other SPARQL query examples are alsoavailable. (PDF 6814 kb)AbbreviationsBMRB: BioMagResBank; MECP2: methyl-CpG-binding protein 2; NMR: nuclearmagnetic resonance; OMIM: Online Mendelian Inheritance in Man; OWL: webontology language; RDF: resource description framework; RDFS: RDF schema;SASA: solvent accessible surface area; SNP: single nucleotide polymorphism;SPARQL: SPARQL Protocol and RDF Query Language; XML: eXtensibleMarkup Language.Competing interestsThe authors declare that they have no competing interests.Authors’ contributionsMY performed research, data analysis and wrote the paper with NK. TF wasprincipal investigator for this project, contributed to research design and feedbackon the manuscript. All authors read and approved the final version of manuscript.AcknowledgementsThis work was supported by National Bioscience Database Center (NBDC) ofJapan Science and Technology (JST); and the United States National Libraryof Medicine [LM05799] and National Institute of General Medical Sciences[GM109046].Author details1Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka565-0871, Japan. 2Department of Biochemistry, University of Wisconsin-Madison,Madison, WI 53706, USA. 3Department of Informatics & Telecommunications,University of Athens, Athens, Greece. 4Department of Computer Sciences,University of Wisconsin-Madison, Madison, WI 53706, USA.Received: 11 July 2015 Accepted: 18 March 2016References1. 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, KentWenger 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 andarchiving. J Chem Inf Comput Sci. 1991;31:326–33.3. Hall SR, Spadaccini N. The STAR File: Detailed Specifications. J Chem InfComput 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-13chemical shift differences and its application to the detection andcorrection of errors in referencing and spin system identifications. J BiomolNMR. 2005;32:13–22.6. Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL. PACSY, a relationaldatabase management system for protein structure and chemical shiftanalysis. 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, DeBrevern 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 27October 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. ProteinData Bank Japan (PDBj): maintaining a structural data archive andresource description framework format. Nucleic Acids Res.2012;40:D453–60.13. Berners-Lee T. Linked Data, In Design Issues: Architectural and PhilosophicalPoints. 2006, http://www.w3.org/DesignIssues/LinkedData. Accessed 27October 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 methylatedDNA. J Mol Biol. 1999;291:1055–65.Yokochi et al. Journal of Biomedical Semantics  (2016) 7:16 Page 4 of 4

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

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

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