The C6H6 NMR repository: An integral solution to control the flow of your data from the magnet to the public
Luc Patiny
Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015 Switzerland
Search for more papers by this authorMichaël Zasso
Institut de Police Scientifique, Ecole des Sciences Criminelles, University of Lausanne, Lausanne, CH-1015 Switzerland
Search for more papers by this authorDaniel Kostro
Institut de Police Scientifique, Ecole des Sciences Criminelles, University of Lausanne, Lausanne, CH-1015 Switzerland
Search for more papers by this authorAndrés Bernal
Departamento de Ciencias Básicas y Modelado, Universidad Jorge Tadeo Lozano, Bogotá, Colombia
Search for more papers by this authorAndrés M. Castillo
Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Cali, Valle, Colombia
Search for more papers by this authorAlejandro Bolaños
Chemistry Department, Universidad del Valle, Cali, Valle, Colombia
Search for more papers by this authorMiguel A. Asencio
Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015 Switzerland
Search for more papers by this authorNorman Pellet
Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015 Switzerland
Search for more papers by this authorMatthew Todd
School of Chemistry, The University of Sydney, Sydney, 2006 NSW, Australia
Search for more papers by this authorNils Schloerer
Department of Chemistry, University of Cologne, Köln, Germany
Search for more papers by this authorStefan Kuhn
Department of Chemistry, University of Cologne, Köln, Germany
Search for more papers by this authorElaine Holmes
Division of Computational and Systems Medicine, Imperial College, London, UK
Search for more papers by this authorSacha Javor
Department of Chemistry and Biochemistry, University of Bern, Bern, 3012 Switzerland
Search for more papers by this authorCorresponding Author
Julien Wist
Chemistry Department, Universidad del Valle, Cali, Valle, Colombia
Correspondence
Julien Wist, Chemistry Department, Universidad del Valle, A.A. 25360, Cali, Valle, Colombia.
Email: [email protected]
Search for more papers by this authorLuc Patiny
Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015 Switzerland
Search for more papers by this authorMichaël Zasso
Institut de Police Scientifique, Ecole des Sciences Criminelles, University of Lausanne, Lausanne, CH-1015 Switzerland
Search for more papers by this authorDaniel Kostro
Institut de Police Scientifique, Ecole des Sciences Criminelles, University of Lausanne, Lausanne, CH-1015 Switzerland
Search for more papers by this authorAndrés Bernal
Departamento de Ciencias Básicas y Modelado, Universidad Jorge Tadeo Lozano, Bogotá, Colombia
Search for more papers by this authorAndrés M. Castillo
Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Cali, Valle, Colombia
Search for more papers by this authorAlejandro Bolaños
Chemistry Department, Universidad del Valle, Cali, Valle, Colombia
Search for more papers by this authorMiguel A. Asencio
Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015 Switzerland
Search for more papers by this authorNorman Pellet
Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015 Switzerland
Search for more papers by this authorMatthew Todd
School of Chemistry, The University of Sydney, Sydney, 2006 NSW, Australia
Search for more papers by this authorNils Schloerer
Department of Chemistry, University of Cologne, Köln, Germany
Search for more papers by this authorStefan Kuhn
Department of Chemistry, University of Cologne, Köln, Germany
Search for more papers by this authorElaine Holmes
Division of Computational and Systems Medicine, Imperial College, London, UK
Search for more papers by this authorSacha Javor
Department of Chemistry and Biochemistry, University of Bern, Bern, 3012 Switzerland
Search for more papers by this authorCorresponding Author
Julien Wist
Chemistry Department, Universidad del Valle, Cali, Valle, Colombia
Correspondence
Julien Wist, Chemistry Department, Universidad del Valle, A.A. 25360, Cali, Valle, Colombia.
Email: [email protected]
Search for more papers by this authorAbstract
NMR is a mature technique that is well established and adopted in a wide range of research facilities from laboratories to hospitals. This accounts for large amounts of valuable experimental data that may be readily exported into a standard and open format. Yet the publication of these data faces an important issue: Raw data are not made available; instead, the information is slimed down into a string of characters (the list of peaks). Although historical limitations of technology explain this practice, it is not acceptable in the era of Internet. The idea of modernizing the strategy for sharing NMR data is not new, and some repositories exist, but sharing raw data is still not an established practice. Here, we present a powerful toolbox built on recent technologies that runs inside the browser and provides a means to store, share, analyse, and interact with original NMR data. Stored spectra can be streamlined into the publication pipeline, to improve the revision process for instance. The set of tools is still basic but is intended to be extended. The project is open source under the Massachusetts Institute of Technology (MIT) licence.
Supporting Information
Filename | Description |
---|---|
MRC_4669-Sup-0001-ELNJSONformatschemadescriptionofacompoundchemicalsample.docxPDF document, 8.8 KB |
Data S1. Software tools and tutorials in liquid-state NMR |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
REFERENCES
- 1M. D. Wilkinson, M. Dumonier, I. J. J. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, J. -W. Boiten, L. Bonino da Silva Santos, P. E. Bourne, J. Bouwman, A. J. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, C. T. Evelo, R. Finkers, A. Gonzalez-Beltran, A. J. G. Gray, P. Groth, C. Goble, J. S. Grethe, J. Heringa, P. A. C’t Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, S. J. Lusher, M. E. Martone, A. Mons, A. L. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, S. -A. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, M. A. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, J. Velterop, A. Waagmeester, P. Wittenburg, K. Wolstencroft, J. Zhao, B. Mons, Sci. Data. 2016, 3, 160018, https://doi.org/10.1038/sdata.2016.18.
- 2A. M. Clark, A. J. Williams, S. Ekins, Aust. J. Chem. 2015, 7, 9, https://doi.org/10.1186/s13321-015-0057-7.
- 3D. Jeannerat, Magn. Reson. Chem. 2016, 55, 7, https://doi.org/10.1002/mrc.4527.
- 4J. Wist, Magn. Reson. Chem. 2016, 55, 22, https://doi.org/10.1002/mrc.4533.
- 5P. Murray-Rust, R. Smith-Unna, D-Lib Mag 2014, 20, https://doi.org/10.1045/november14-murray-rust.
- 6Murray-Rust P. Save our spectra. https://blogs.ch.cam.ac.uk/pmr/2007/08/12/save-our-spectra/. june 9, 2017.
- 7G. F. Pauli, M. Niemitz, J. Bisson, M. W. Lodewyk, C. Soldi, J. T. Shaw, D. J. Tantillo, J. M. Saya, K. Vos, R. A. Kleinnijenhuis, H. Hiemstra, S.-N. Chen, J. B. McAlpine, D. C. Lankin, J. B. Friesen, J Org Chem 2016, 81, 878, https://doi.org/10.1021/acs.joc.5b02456.
- 8D. Banfi, L. Patiny, Chimia 2008, 62, 280, https://doi.org/10.2533/chimia.2008.280.
- 9A. Eklund, T. E. Nichols, H. Knutsson, Proc Natl Acad Sci 2016, 113, 7900, https://doi.org/10.1073/pnas.1602413113.
- 10J. Bisson, C. Simmler, S.-N. Chen, J. Brent Friesen, D. C. Lankin, J. B. McAlpine, G. F. Pauli, Nat. Prod. Rep. 2016, 33, 1028, https://doi.org/10.1039/c6np00022c.
- 11W. Robien, Trac-Trend Anal Chem 2009, 28, 914, https://doi.org/10.1016/j.trac.2009.03.012.
- 12 NMR guidelines for ACS journals. http://pubs.acs.org/paragonplus/submission/acs_nmr_guidelines.pdf. September 21, 2017.
- 13K. A. Badiola, D. H. Quan, J. A. Triccas, M. H. Todd, PLoS One 2014, 9, e111782, https://doi.org/10.1371/journal.pone.0111782.
- 14J. L. Pons, T. E. Malliavin, D. Tramesel, M. A. Delsuc, Bioinformatics 2004, 20, 3707, https://doi.org/10.1093/bioinformatics/bth450.
- 15J. G. Napolitano, D. C. Lankin, T. N. Graf, J. Brent Friesen, S. N. Chen, J. B. McAlpine, N. H. Oberlies, G. F. Pauli, J Org Chem 2013, 78, 2827, https://doi.org/10.1021/jo302720h.
- 16C. Steinbeck, S. Krause, S. Kuhn, J. Chem. Inf. Comput. Sci. 2003, 43, 1733.
- 17S. Kuhn, N. E. Schlörer, Magn. Reson. Chem. 2015, 53, 582, https://doi.org/10.1002/mrc.4263.
- 18 NMRShiftDB. website. http://nmrshiftdb.org. June 21, 2017.
- 19N. Haider, W. Robien, Nachr Chem 2016, 64, 196, https://doi.org/10.1002/nadc.20164047147.
- 20 CSEARCH/NMRPREDICT-Server. http://nmrpredict.orc.univie.ac.at/. June 21, 2017.
- 21 Wiley SSR. https://www.wsslabs.com. July 4, 2017.
- 22Y. Binev, M. M. Marques, J. Aires-de-Sousa, J. Chem. Inf. Model. 2007, 47, 2089, https://doi.org/10.1021/ci700172n.
- 23 SPINUS. website. http://www2.chemie.uni-erlangen.de/services/spinus/. June 1, 2017.
- 24 ACD/LABS NMR shift predict webpage. http://www.acdlabs.com/products/adh/nmr/nmr_pred/. June 23, 2017.
- 25A. M. Castillo, L. Patiny, J. Wist, J. Magn. Reson. 2011, 209, 123, https://doi.org/10.1016/j.jmr.2010.12.008.
- 26A. M. Castillo, A. Bernal, R. Dieden, L. Patiny, J. Wist, Aust. J. Chem. 2016, 8, 26, https://doi.org/10.1186/s13321-016-0134-6.
- 27R. P. Verma, C. Hansch, Chem. Rev. 2011, 111, 2865, https://doi.org/10.1021/cr100125d.
- 28D. Tulpan, S. Léger, L. Belliveau, A. Culf, M. Cuperlović-Culf, BMC Bioinform 2011, 12, 400, https://doi.org/10.1186/1471-2105-12-400.
- 29K. Bingol, L. Bruschweiler-Li, D. Li, B. Zhang, M. Xie, R. Brüschweiler, Bioanalysis 8, 557, https://doi.org/10.4155/bio-2015-0004.
- 30 SDBSWeb. http://sdbs.db.aist.go.jp (National Institute of Advanced Industrial Science and Technology) June 21, 2017.
- 31 Chemspider website. www.chemspider.com. June 21, 2017.
- 32D. S. Wishart, T. Jewison, A. C. Guo, M. Wilson, C. Knox, Y. Liu, Y. Djoumbou, R. Mandal, F. Aziat, E. Dong, S. Bouatra, I. Sinelnikov, D. Arndt, J. Xia, P. Liu, F. Yallou, T. Bjorndahl, R. Perez-Pineiro, R. Eisner, F. Allen, V. Neveu, R. Greiner, A. Scalbert, Nucleic Acids Res. 2013, 41(D1), D801.
- 33 The Human Metabolome Database. http://www.hmdb.ca/. June 21, 2017.
- 34E. L. Ulrich, H. Akutsu, J. F. Doreleijers, Y. Harano, Y. E. Ioannidis, J. Lin, M. Livny, S. Mading, D. Maziuk, Z. Miller, E. Nakatani, C. F. Schulte, D. E. Tolmie, R. K. Wenger, H. Yao, J. L. Markley, Nucleic Acids Res. 2008, 36, D402, https://doi.org/10.1093/nar/gkm957.
- 35 Biological Magnetic Resonance Data Bank website. http://www.bmrb.wisc.edu/. June 21, 2017.
- 36 SPECTRa website. https://spectradspace.lib.imperial.ac.uk:8443/handle/10042/25. June 27, 2017.
- 37S. J. Chalk, Aust. J. Chem. 2016, 8, 55, https://doi.org/10.1186/s13321-016-0170-2.
- 38 CouchDB website. http://couchdb.apache.org/. June 29, 2017.
- 39 JavaScript Object Notation Description. https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/JSON. June 29, 2017.
- 40 rest-on-couch project source. https://github.com/cheminfo/rest-on-couch. June 29, 2017.
- 41 Cheminfo sources. https://github.com/cheminfo. June 29, 2017.
- 42 Lactame.com libraries. www.lactame.com. June 29, 2017.
- 43https://www.npmjs.com/search?q=maintainer:cheminfo-bot. June 29, 2017.
- 44 Cheminfo-js sources. https://github.com/cheminfo-js June 29, 2017.
- 45 mljs sources. https://github.com/mljs. June 29, 2017.
- 46 DataWarrior website. http://www.openmolecules.org/datawarrior. June 1, 2017.
- 47C. Cobas, F. Seoane, S. Domínguez, S. Sykora, A. N. Davies, Spectrosc. Eur. 2011, 23, 26.
- 48L. Belaid, W. Mourou, Image Anal Stereol 2011, 28, 93, https://doi.org/10.5566/ias.v28.p93-102.
10.5566/ias.v28.p93-102 Google Scholar
- 49J. Canny, IEEE T Pattern Anal 1986, 6, 679.
- 50 Visualizer project source. https://github.com/npellet/visualizer June 29, 2017.
- 51 NMR Suite AU Programs Reference Manual, Bruker Analytik GmbH, Rheinstetten 1999.
- 52 Jython website. http://www.jython.org/. July 4, 2017.
- 53 roc-eln-docker project source. https://github.com/cheminfo/roc-eln-docker. June 29, 2017.
- 54 Docker website. https://www.docker.com/. June 29, 2017.
- 55R. K. Rew, G. P. Davis, IEEE Comput Grap 1990, 10, 76.
- 56 NetCDF website. https://www.unidata.ucar.edu/software/netcdf/. July 4, 2017.
- 57B. Bienfait, P. Ertl, Aust. J. Chem. 2013, 5, 24.
- 58 ImageCLEF@ICPR website. http://www.imageclef.org/2010/ICPR. June 7, 2017.
- 59A. E. Williamson, P. M. Ylioja, M. N. Robertson, Y. Antonova-Koch, V. Avery, J. B. Baell, H. Batchu, S. Batra, J. N. Burrows, S. Bhattacharyya, F. Calderon, S. A. Charman, J. Clark, B. Crespo, M. Dean, S. L. Debbert, M. Delves, A. S. M. Dennis, F. Deroose, S. Duffy, S. Fletcher, G. Giaever, I. Hallyburton, F.-J. Gamo, M. Gebbia, R. Kiplin Guy, Z. Hungerford, K. Kirk, M. J. Lafuente-Monasterio, A. Lee, S. Meister, C. Nislow, J. P. Overington, G. Papadatos, L. Patiny, J. Pham, S. A. Ralph, A. Ruecker, E. Ryan, C. Southan, K. Srivastava, C. Swain, M. J. Tarnowski, P. Thomson, P. Turner, I. M. Wallace, T. N. C. Wells, K. White, L. White, P. Willis, E. A. Winzeler, S. Wittlin, M. H. Todd, ACS Cent Sci 2016, 2, 687, https://doi.org/10.1021/acscentsci.6b00086.