Crystallography Open Database: History, Development, and Perspectives

=2232675 (accessed 19 April 2019). 36 Eysenbach, G. (2006). Citation advantage of open access articles. PLoS Biol. 4 (5): e157. https://doi.org/10.1371/journal.pbio.0040157. 37 Harnad, S. and Brody, T. (2004). Comparing the impact of Open Access (OA) vs. Non-OA articles in the same journals. D-Lib Magaz. 10 (6): https://doi .org/10.1045/june2004-harnad. 38 Harnad, S., Brody, T., Vallières, F. et al. (2008). The access/impact problem and the green and gold roads to open access: an update. Serials Rev. 34 (1): 36–40. https://doi.org/10.1080/00987913.2008.10765150. 36 1 Crystallography Open Database: History, Development, and Perspectives 39 Zucker, L.G., Darby, M.R., Furner, J., et al. (2006). Minerva unbound: knowledge stocks, knowledge flows and new knowledge production. NBER Working Paper Series. http://www.nber.org/papers/w12669 (accessed 19 April 2019). 40 Piwowar, H.A. and Vision, T.J. (2013). Data reuse and the open data citation advantage. PeerJ 1: e175. https://doi.org/10.7717/peerj.175. 41 Galperin, M.Y. and Cochrane, G.R. (2010). The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. Nucleic Acids Res. 39 (Database): D1–D6. https://doi.org/10.1093/nar/gkq1243. 42 IUCr (2016). CIF version 1.1 working specification. http://www.iucr.org/ resources/cif/spec/version1.1 (accessed 06 November 2016, 14:55 EET). 43 Merkys, A., Vaitkus, A., Butkus, J. et al. (2016). COD::CIF::Parser: an error-correcting CIF parser for the Perl language. J. Appl. Crystallogr. 49 (1): 292–301. https://doi.org/10.1107/S1600576715022396. 44 Berman, H.M., Westbrook, J., Feng, Z. et al. (2000). The Protein Data Bank. Nucleic Acids Res. 28: 235–242. https://doi.org/10.1093/nar/28.1.235. 45 Day, N., Downing, J., Adams, S. et al. (2012). CrystalEye: automated aggregation, semantification and dissemination of the world’s open crystallographic data. J. Appl. Crystallogr. 45: 316–323. https://doi.org/10.1107/

[1]  Hans Wondratschek,et al.  Bilbao Crystallographic Server: I. Databases and crystallographic computing programs , 2006 .

[2]  Pierre Baldi Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response to the Letter by the Cambridge Crystallographic Data Centre , 2011, J. Chem. Inf. Model..

[3]  Robert T. Downs,et al.  Building the American Mineralogist Crystal Structure Database: A recipe for construction of a small Internet database , 2006 .

[4]  Peter Moeck,et al.  3D printed models of small and large molecules, structures and morphologies of crystals, as well as their anisotropic physical properties , 2015 .

[5]  Xavier Gonze,et al.  Sharing electronic structure and crystallographic data with ETSF_IO , 2008, Comput. Phys. Commun..

[6]  James R. Hester A validating CIF parser: PyCIFRW , 2006 .

[7]  I. D. Brown,et al.  Classification and use of electron density data , 2006 .

[8]  Gary L Gilliland,et al.  The Biological Macromolecule Crystallization Database: crystallization procedures and strategies. , 2002, Acta crystallographica. Section D, Biological crystallography.

[9]  Robert T. Downs,et al.  The power of databases: The RRUFF project , 2016 .

[10]  F. Allen,et al.  The crystallographic information file (CIF) : a new standard archive file for crystallography , 1991 .

[11]  R. Downs Topology of the pyroxenes as a function of temperature, pressure, and composition as determined from the procrystal electron density , 2003 .

[12]  Saulius Gražulis,et al.  Specification of the Crystallographic Information File format, version 2.0 , 2016 .

[13]  Robin Taylor,et al.  Deducing chemical structure from crystallographically determined atomic coordinates , 2011, Acta crystallographica. Section B, Structural science.

[14]  Antony J. Williams,et al.  ChemSpider:: An Online Chemical Information Resource , 2010 .

[15]  S. Harnad,et al.  Comparing the Impact of Open Access (OA) vs. Non-OA Articles in the Same Journals , 2004 .

[16]  Duncan H. Gregory,et al.  The Search for Hydrogen Stores on a Large Scale; A Straightforward and Automated Open Database Analysis as a First Sweep for Candidate Materials , 2015 .

[17]  Saulius Gražulis,et al.  AceDRG: a stereochemical description generator for ligands , 2017, Acta crystallographica. Section D, Structural biology.

[18]  P. Villarsa,et al.  The Pauling File , Binaries Edition , 2004 .

[19]  Marc Scheufen,et al.  The determinants of open access publishing: survey evidence from Germany , 2013 .

[20]  Saulius Gražulis,et al.  Validation and extraction of molecular-geometry information from small-molecule databases , 2017, Acta crystallographica. Section D, Structural biology.

[21]  Henry Pillière,et al.  Full-profile search–match by the Rietveld method , 2019, Journal of applied crystallography.

[22]  Daniel Chateigner,et al.  MPOD: A Material Property Open Database linked to structural information , 2012 .

[23]  Peter Murray-Rust,et al.  CrystalEye: automated aggregation, semantification and dissemination of the world's open crystallographic data , 2012 .

[24]  Roy Fielding,et al.  Architectural Styles and the Design of Network-based Software Architectures"; Doctoral dissertation , 2000 .

[25]  Peter Moeck,et al.  3D printing of representation surfaces from tensor data of KH2PO4 and low-quartz utilizing the WinTensor software , 2015 .

[26]  G. Langlet,et al.  International Tables for Crystallography , 2002 .

[27]  Kimito Funatsu,et al.  Further development of structure generation in the automated structure elucidation system CHEMICS , 1988, J. Chem. Inf. Comput. Sci..

[28]  Armel Le Bail,et al.  Inorganic structure prediction with GRINSP , 2005 .

[29]  Fei Long,et al.  REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. , 2004, Acta crystallographica. Section D, Biological crystallography.

[30]  John Faber,et al.  The Powder Diffraction File: present and future. , 2002, Acta crystallographica. Section B, Structural science.

[31]  R. Downs,et al.  The American Mineralogist crystal structure database , 2003 .

[32]  Matt Zandstra,et al.  Version Control with Subversion , 2010 .

[33]  Colin R. Groom,et al.  A crystallographic perspective on sharing data and knowledge , 2014, Journal of Computer-Aided Molecular Design.

[34]  Jill P Mesirov,et al.  Accessible Reproducible Research , 2010, Science.

[35]  C. Oppenheim,et al.  The Access/Impact Problem and the Green and Gold Roads to Open Access: An Update , 2008 .

[36]  A. R. Srinivasan,et al.  The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. , 1992, Biophysical journal.

[37]  Heather A. Piwowar,et al.  Data reuse and the open data citation advantage , 2013, PeerJ.

[38]  Luc Moreau,et al.  The Open Provenance Model , 2007 .

[39]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[40]  Frank H. Allen,et al.  Cambridge Structural Database , 2002 .

[41]  Emre S. Tasci,et al.  Symmetry-Based Computational Tools for Magnetic Crystallography , 2015 .

[42]  Fei Long,et al.  A new generation of CCP4 monomer library based on Crystallography Open Database , 2014 .

[43]  R. Rechenmacher,et al.  The Sloan Digital Sky Survey data acquisition system, and early results , 1999, 1999 IEEE Conference on Real-Time Computer Applications in Nuclear Particle and Plasma Physics. 11th IEEE NPSS Real Time Conference. Conference Record (Cat. No.99EX295).

[44]  Peter Moeck,et al.  One-click preparation of 3D print files (*.stl, *.wrl) from *.cif (crystallographic information framework) data using Cif2VRML , 2014, Powder Diffraction.

[45]  Shuichi Iwata,et al.  The Linus Pauling file (LPF) and its application to materials design , 1998 .

[46]  Herbert J. Bernstein,et al.  VCIF2: extended CIF validation software , 2008 .

[47]  Peter Ertl,et al.  JSME: a free molecule editor in JavaScript , 2013, Journal of Cheminformatics.

[48]  Dieter Van Uytvanck,et al.  Identification of Reproducible Subsets for Data Citation, Sharing and Re-Use , 2016, Bull. IEEE Tech. Comm. Digit. Libr..

[49]  Saulius Gražulis,et al.  Crystallography Open Database – an open-access collection of crystal structures , 2009, Journal of applied crystallography.

[50]  Boris Kozinsky,et al.  AiiDA: Automated Interactive Infrastructure and Database for Computational Science , 2015, ArXiv.

[51]  Haruki Nakamura,et al.  The Protein Data Bank at 40: reflecting on the past to prepare for the future. , 2012, Structure.

[52]  Saulius Gražulis,et al.  Computing stoichiometric molecular composition from crystal structures , 2015, Journal of applied crystallography.

[53]  Saulius Gražulis,et al.  COD::CIF::Parser: an error-correcting CIF parser for the Perl language , 2016, Journal of applied crystallography.

[54]  L. Zucker,et al.  Minerva Unbound: Knowledge Stocks, Knowledge Flows and New Knowledge Production , 2006 .

[55]  Werner Kaminsky,et al.  From CIF to virtual morphology using the WinXMorph program , 2007 .

[56]  Peter Moeck,et al.  Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration , 2011, Nucleic Acids Res..

[57]  Olivier Dalle,et al.  On reproducibility and traceability of simulations , 2012, Proceedings Title: Proceedings of the 2012 Winter Simulation Conference (WSC).

[58]  P. Luksch,et al.  New developments in the Inorganic Crystal Structure Database (ICSD): accessibility in support of materials research and design. , 2002, Acta crystallographica. Section B, Structural science.

[59]  Andreas Rauber,et al.  DEPRECATED: Data Citation of Evolving Data: Recommendations of the Working Group on Data Citation (WGDC) , 2016 .

[60]  Luc Moreau,et al.  The Open Provenance Model: An Overview , 2008, IPAW.

[61]  Saulius Gražulis,et al.  Crystallographic education in the 21st century , 2015, Journal of applied crystallography.

[62]  J. E. Chisholm,et al.  International Tables for Crystallography, Vol. A: Space-group Symmetry , 1984, Mineralogical Magazine.

[63]  Daniel Chateigner,et al.  Implementing graphic outputs for the Material Properties Open Database (MPOD) , 2014 .

[64]  Chris Morley,et al.  Open Babel: An open chemical toolbox , 2011, J. Cheminformatics.

[65]  Brian H. Toby,et al.  CIF applications. XIV. Reporting of Rietveld results using pdCIF: GSAS2CIF , 2003 .

[66]  Armel Le Bail,et al.  Inorganic structure prediction with GRINSP , 2005 .

[67]  John D. Westbrook,et al.  The Nucleic Acid Database: new features and capabilities , 2013, Nucleic Acids Res..

[68]  J. Rodgers,et al.  CRYSTMET: a database of the structures and powder patterns of metals and intermetallics. , 2002, Acta crystallographica. Section B, Structural science.

[69]  Philip E. Bourne,et al.  Macromolecular dictionary (mmCIF) , 2006 .

[70]  T. Hahn International Tables for Crystallography: Space-group symmetry , 2006 .

[71]  Saulius Gražulis,et al.  Raman Open Database: first interconnected Raman–X-ray diffraction open-access resource for material identification , 2019, Journal of applied crystallography.

[72]  Charles Oppenheim,et al.  The citation advantage of open-access articles , 2008, J. Assoc. Inf. Sci. Technol..

[73]  M. Deem,et al.  A biased Monte Carlo scheme for zeolite structure solution , 1998, cond-mat/9809085.

[74]  Peter Moeck,et al.  3D PRINTED MODELS OF MATERIALS TENSOR REPRESENTATIONS AND THE CRYSTAL MORPHOLOGY OF ALPHA QUARTZ , 2016 .

[75]  Paul D. Adams,et al.  iotbx.cif: a comprehensive CIF toolbox , 2011, Journal of applied crystallography.

[76]  Pierre Baldi,et al.  Small-Molecule 3D Structure Prediction Using Open Crystallography Data , 2013, J. Chem. Inf. Model..

[77]  A. Kirov,et al.  Crystallography online: Bilbao Crystallographic Server , 2017 .

[78]  Peter Moeck,et al.  Crystal structure visualizations in three dimensions with database support , 2005 .

[79]  C. Michael Pilato,et al.  Version control with subversion - next generation open source version control , 2004 .