% This file was created with JabRef 2.5. % Encoding: UTF8 @ARTICLE{Allen1979, author = {Allen, F. H. and Bellard, S. and Brice, M. D. and Cartwright, B. A. and Doubleday, A. and Higgs, H. and Hummelink, T. and Hummelink-Peters, B. G. and Kennard, O. and Motherwell, W. D. S. and Rodgers, J. R. and Watson, D. G.}, title = {{The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information}}, journal = {Acta Crystallographica Section B}, year = {1979}, volume = {35}, pages = {2331--2339}, number = {10}, month = {Oct}, doi = {10.1107/S0567740879009249}, url = {http://dx.doi.org/10.1107/S0567740879009249} } @ARTICLE{Berman2002, author = {Berman, Helen M. and Battistuz, Tammy and Bhat, T. N. and Bluhm, Wolfgang F. and Bourne, Philip E. and Burkhardt, Kyle and Feng, Zukang and Gilliland, Gary L. and Iype, Lisa and Jain, Shri and Fagan, Phoebe and Marvin, Jessica and Padilla, David and Ravichandran, Veerasamy and Schneider, Bohdan and Thanki, Narmada and Weissig, Helge and Westbrook, John D. and Zardecki, Christine}, title = {{The Protein Data Bank}}, journal = {Acta Crystallographica Section D}, year = {2002}, volume = {58}, pages = {899--907}, number = {6 Part 1}, month = {Jun}, doi = {10.1107/S0907444902003451}, url = {http://dx.doi.org/10.1107/S0907444902003451} } @ARTICLE{Berman1992, author = {H. M. Berman and W. K. Olson and D. L. Beveridge and J. Westbrook and A. Gelbin and T. Demeny and S.-H. Hsieh and A. R. Srinivasan and B. Schneider}, title = {The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids}, journal = {Biophys. J.}, year = {1992}, volume = {63}, pages = {751-759}, owner = {saulius}, timestamp = {2011.07.31} } @ARTICLE{Bernstein1977, author = {F. C. Bernstein and T. F. Koetzle and G. J. Williams and E. F. Meyer and M. D. Brice and J. R. Rodgers and O. Kennard and T. Shimanouchi and M. Tasumi}, title = {The Protein Data Bank: a computer-based archival file for macromolecular structures.}, journal = {J. Mol. Biol.}, year = {1977}, volume = {112}, pages = {535--542}, number = {3}, month = {May}, keywords = {Computers; Great Britain; Information Systems; Japan; Protein Conformation; Proteins; United States}, owner = {bricehoffmann}, pmid = {875032}, timestamp = {2009.02.13} } @BOOK{Collins-Sussman2008, title = {Version Control with Subversion}, publisher = {O'Reilly Media}, year = {2008}, author = {Collins-Sussman, Ben and Fitzpatrick, Brian W and Pilato, C Michael}, url = {\href{http://svnbook.red-bean.com/} {http://svnbook.red-bean.com/}} } @PHDTHESIS{Day2008, author = {Nicholas Elliot Day}, title = {Automated Analysis and Validation of Open Chemical Data}, school = {University of Cambridge}, year = {2008}, month = {nov}, abstract = {Methods to automatically extract Open Data from the chemical literature, validate it, and use it to validate theory are examined. Chemical identifiers which assist the automatic location of chemical struc- tures using commercial Web search engines are investigated. The IUPAC International Chemical Idenfitifer (InChI) gives almost 100% recall and pre- cision, though is shown to be too long for present search engines. A com- bination of InChI and InChIKey, a shorter, fixed-length hash of the InChI string, is concluded to be the best current method of identifying structures. The proportion of published, Open Crystallographic Information Files (CIFs) that are valid with respect to the specification is shown to be im- proving, and is around 99% in 2007. The error rate in the conversion of valid CIFs to Chemical Markup Language (CML) is less than 0.2%. The machine generation of connection tables from CIFs requires many heuristics, and in some cases it is impossible to deduce the exact connection table. CrystalEye, a fully-automated system for the reformulation of the frag- mented crystallographic Web into a structured XML-based repository is de- scribed. Published, Open CIFs can be located and aggregated programmat- ically with almost 100% recall. It is shown that, by converting CIF data to CML, software can be created to use the latest Web standards and tech- nologies to enhance the ability of Web users to browse, find, keep updated, download and reuse the latest published crystallography. A workflow for the high-throughput calculation of solid-state geometry using a semi-empirical method is described. A wide-range of organic and inorganic systems provided by CrystalEye are used to test both the data and the method. Several errors in the method are discovered, many of which can be attributed to the parameterization process. An Open NMR experiment to perform high-throughput prediction of 13 C chemical shifts using a GIAO protocol is described. The data and analysis were provided on publicly-available webpages to enable crowdsourcing, which assisted in discovering an error rate of 6.1% in the starting data. The protocol was refined during the work and shown to have an average unsigned error of 2.24ppm for 13 C nuclei of small, rigid molecules; comparable to the errors observed elsewhere for general structures using HOSE and Neural Network methods.}, file = {2008_Day_phdthesis.pdf:by-author/D/Day/2008_Day_phdthesis.pdf:PDF}, keywords = {data management, xray-crystallography, crystallography, NMR}, owner = {saulius}, timestamp = {2013.09.19}, url = {https://www.repository.cam.ac.uk/bitstream/handle/1810/238467/ned24-thesis-corrected-1_A1b.pdf?sequence=1} } @ARTICLE{Downs2003, author = {Downs, RT and Hall-Wallace, M}, title = {The American Mineralogist crystal structure database}, journal = {American Mineralogist}, year = {2003}, volume = {88}, pages = {247-250} } @ARTICLE{Grazulis2009, author = {Gra{\v{z}}ulis, Saulius and Chateigner, Daniel and Downs, Robert T. and Yokochi, A. F. T. and Quir{\'{o}}s, Miguel and Lutterotti, Luca and Manakova, Elena and Butkus, Justas and Moeck, Peter and Le Bail, Armel}, title = {{Crystallography Open Database {--} an open-access collection of crystal structures}}, journal = {Journal of Applied Crystallography}, year = {2009}, volume = {42}, pages = {726--729}, number = {4}, month = {Aug}, doi = {10.1107/S0021889809016690}, url = {http://dx.doi.org/10.1107/S0021889809016690} } @ARTICLE{Grazulis2012, author = {Gražulis, Saulius and Daškevič, Adriana and Merkys, Andrius and Chateigner, Daniel and Lutterotti, Luca and Quirós, Miguel and Serebryanaya, Nadezhda R. and Moeck, Peter and Downs, Robert T. and Le Bail, Armel}, title = {{C}rystallography {O}pen {D}atabase ({COD}): an open-access collection of crystal structures and platform for world-wide collaboration}, journal = {Nucleic Acids Research}, year = {2012}, volume = {40}, pages = {D420-D427}, number = {D1}, month = {Jan}, abstract = {Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.}, doi = {10.1093/nar/gkr900}, file = {:by-author/G/Gražulis/2012_Gražulis_D420.pdf:PDF}, owner = {saulius}, timestamp = {2011.12.29}, url = {http://nar.oxfordjournals.org/content/40/D1/D420.abstract} } @ARTICLE{Grosse-Kunstleve2002, author = {Grosse-Kunstleve, Ralf W. and Sauter, Nicholas K. and Moriarty, Nigel W. and Adams, Paul D.}, title = {{The {\it Computational Crystallography Toolbox}: crystallographic algorithms in a reusable software framework}}, journal = {Journal of Applied Crystallography}, year = {2002}, volume = {35}, pages = {126--136}, number = {1}, month = {Feb}, doi = {10.1107/S0021889801017824}, url = {http://dx.doi.org/10.1107/S0021889801017824} } @ARTICLE{Hall1991, author = {Hall, S. R. and Allen, F. H. and Brown, I. D.}, title = {{The crystallographic information file (CIF): a new standard archive file for crystallography}}, journal = {Acta Crystallographica Section A}, year = {1991}, volume = {47}, pages = {655--685}, number = {6}, month = {Nov}, doi = {10.1107/S010876739101067X}, url = {http://dx.doi.org/10.1107/S010876739101067X} } @ARTICLE{Kabekkodu2002, author = {Kabekkodu, SN and Faber, J and Fawcett, T}, title = {New Powder Diffraction File (PDF-4) in relational database format: advantages and data-mining capabilities}, journal = {Acta Crystallographica, Section B}, year = {2002}, volume = {58}, pages = {333-7} } @ARTICLE{Kaduk2002, author = {Kaduk, James A}, title = {Use of the Inorganic Crystal Structure Database as a problem solving tool}, journal = {Acta Crystallogr B}, year = {2002}, volume = {58}, pages = {370-9}, number = {Pt 3 Pt 1}, month = {Jun}, abstract = {The information in the Inorganic Crystal Structure Database (ICSD) can be used to determine the structures of new compounds by analogy; this database is thus a useful tool for practical problem solving. A model for the structure of (NH(4))Fe(CO(3))(OH)(2) [Cmcm, a = 6.6154 (6), b = 12.0639 (10), c = 6.0263 (5) A, Z = 4] was found by searching the ICSD for compounds with C-centered orthorhombic cells and containing C, H, N and O. [Al(H(2)O)(6)](2)[Al(H(2)O)(5)(SO(4))](2)-(H(3)O)(2)(SO(4))(5) [P1;, a = 12.5881 (5), b = 13.0726 (5), c = 7.3354 (2) A, alpha = 108.162 (2), beta = 70.536 (2), gamma = 112.658 (2) degrees, Z = 1] is isostructural to a Cr compound of the same stoichiometry, which was located by searching on the formula type ANX = A4B7X52. Suitable models for MgCl(2)(H(2)O)(4) [P2(1)/c, a = 5.9001 (9), b = 7.2709 (7), c = 8.4199 (7) A, beta = 111.007 (15) degrees, Z = 2], MgCl(2)(H(2)O)(2) [C2/m, a = 7.3886 (29), b = 8.5498 (24), c = 3.6488 (17) A, beta = 98.96 (3) degrees, Z = 2], and MgCl(2)(H(2)O) [Pnma, a = 8.899 (7), b = 3.6339 (20), c = 11.398 (8) A, Z = 4] were located by combining searches on chemistry and formula type. Quantum-chemical calculations were performed on all five structures to locate the H-atom positions and to obtain quantitative understanding of the hydrogen bonding important in all the structures.}, address = {BP Chemicals, PO Box 3011, MC F-9, Naperville, IL 60566, USA. kadukja@bp.com}, bibliography-url = {http://view.ncbi.nlm.nih.gov/pubmed/12037358}, isbn = {0108-7681} } @INCOLLECTION{Downs2006, author = {Rajan, H. and Uchida, H. and Bryan, D.L. and Swaminathan, R. and Downs, R.T. and Hall-Wallace, M}, title = {Building the American Mineralogist Crystal Structure Database: A recipe for construction of a small Internet database}, booktitle = {Geoinformatics: Data to Knowledge}, year = {2006}, editor = {Sinha, A.K.}, volume = {397}, pages = {73-80}, journal = {Geological Society of America Special Paper} } @ARTICLE{Todorov2008, author = {Todorov, Georgi and Bernstein, Herbert J.}, title = {{{\it VCIF2}: extended CIF validation software}}, journal = {Journal of Applied Crystallography}, year = {2008}, volume = {41}, pages = {808--810}, number = {4}, month = {Aug}, doi = {10.1107/S002188980801385X}, url = {http://dx.doi.org/10.1107/S002188980801385X} } @ARTICLE{Wang2010, author = {Wang, Yanli and Bolton, Evan and Dracheva, Svetlana and Karapetyan, Karen and Shoemaker, Benjamin A. and Suzek, Tugba O. and Wang, Jiyao and Xiao, Jewen and Zhang, Jian and Bryant, Stephen H.}, title = {An overview of the PubChem BioAssay resource}, journal = {Nucleic Acids Research}, year = {2010}, volume = {38}, pages = {D255-D266}, number = {suppl 1}, abstract = {The PubChem BioAssay database (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological activities of small molecules and small interfering RNAs (siRNAs) hosted by the US National Institutes of Health (NIH). It archives experimental descriptions of assays and biological test results and makes the information freely accessible to the public. A PubChem BioAssay data entry includes an assay description, a summary and detailed test results. Each assay record is linked to the molecular target, whenever possible, and is cross-referenced to other National Center for Biotechnology Information (NCBI) database records. ‘Related BioAssays’ are identified by examining the assay target relationship and activity profile of commonly tested compounds. A key goal of PubChem BioAssay is to make the biological activity information easily accessible through the NCBI information retrieval system-Entrez, and various web-based PubChem services. An integrated suite of data analysis tools are available to optimize the utility of the chemical structure and biological activity information within PubChem, enabling researchers to aggregate, compare and analyze biological test results contributed by multiple organizations. In this work, we describe the PubChem BioAssay database, including data model, bioassay deposition and utilities that PubChem provides for searching, downloading and analyzing the biological activity information contained therein.}, doi = {10.1093/nar/gkp965}, eprint = {http://nar.oxfordjournals.org/content/38/suppl_1/D255.full.pdf+html}, url = {http://nar.oxfordjournals.org/content/38/suppl_1/D255.abstract} } @ARTICLE{White2002, author = {White, Peter S and Rodgers, John R and Le Page, Yvon}, title = {CRYSTMET: a database of the structures and powder patterns of metals and intermetallics}, journal = {Acta Crystallogr B}, year = {2002}, volume = {58}, pages = {343-8}, number = {Pt 3 Pt 1}, month = {Jun}, abstract = {CRYSTMET is a database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) and associated bibliographic, chemical and physical information. Also included are simulated powder diffraction patterns for all of the entries. The database currently contains almost 70,000 entries and covers the literature exhaustively from 1922 to the present. The database is available on CD-ROM with search/analysis software for use on personal computers. This software can be used with any database in the appropriate format; currently CRYSTMET and the ICSD databases are available. This paper describes the database content, the procedures used in its construction, the software made available to the user and a number of potential uses for the data.}, address = {Department of Chemistry, CB 3290 Venable Hall, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA. pwhite@pyrite.chem.unc.edu}, bibliography-url = {http://view.ncbi.nlm.nih.gov/pubmed/12037354}, isbn = {0108-7681} } @TECHREPORT{Zucker2006, author = {Lynne G. Zucker and Michael R. Darby and Jonathan Furner and Robert C. Liu and Hongyan Ma}, title = {Minerva Unbound: Knowledge Stocks, Knowledge Flows and New Knowledge Production}, institution = {National Bureau of Economic Research}, year = {2006}, type = {Working Paper}, number = {12669}, month = {November}, abstract = {The rate of regional growth of new knowledge in the field of nanotechnology, as measured by counts of articles and patents in the open-access digital library NanoBank, is shown to be positively affected both by the size of existing regional stocks of recorded knowledge in all scientific fields, and the extent to which tacit knowledge in all fields flows between institutions of different organizational types. The level of federal funding has a large, robust impact on both publication and patenting. The data provide further support for the cumulative advantage model of knowledge production, and for ongoing efforts to institutionalize channels through which cross-organizational collaboration may be achieved.}, series = {Working Paper Series}, url = {http://www.nber.org/papers/w12669} } @ELECTRONIC{Perl2008, year = {2008}, title = {Perl.org}, note = {accessed \mbox{2011-10-20}}, url = {http://www.perl.org/}, abstract = {Perl.com includes resources on downloading and installing Perl, a six-part tutorial on learning Perl, Perl articles, and Perl weblogs to help new and experienced programmers refine their skills, solve problems, and contribute to the worldwide Perl community}, key = {Perl}, publisher = {O’Reilly Media} } @MISC{Rsync2008, title = {Rsync}, year = {2008}, note = {accessed \mbox{2008-09-01}}, key = {Rsync}, url = {\href{http://samba.anu.edu.au/rsync/} {http://samba.anu.edu.au/rsync/}} }