Chemical Informatics Letters

Volume 13, Issue 1; July 2006

Editor: Jonathan M Goodman

ISSN 1752-0010

Definition and exchange of crystallographic data
International Tables for Crystallography: Volume G: Definition and exchange of crystallographic data, edited by Sydney Hall and Brian McMahon, is now available from the International Union of Crystallography. Crystallographers lead the world in the precise recording of molecular scientific information, and this book provides an authoritative definition of the key file formats, focussing particularly on the Crystallographic Information File (CIF). The accompanying CD-ROM contains the CIF dictionaries in machine-readable form and a collection of libraries and utility programs.

This is a substantial book with nearly six hundred pages. This is necessary, because the book lists all the possible dictionary entries in the CIF format, in order to define all of the terms precisely and to address all of the detail required to rigorously cover all of the issues involved in crystallography. Some of the detail could perhaps have been abbreviated. For example, a detailed account of the CIF data dictionaries takes up about half the book, and this lists separately all the elements of the matrices and vectors in the data dictionaries, and sometimes these differ only in the indices. However, where this book errs, it is on the side of excessive detail and never risks losing precision by saving space. This bias is essential for a definitive reference work.

The book starts with a historical account of the development of CIF files, and then gives an account of the concepts and specifications for CIF files and related formats. Data definition and classification forms a major section, followed by a detailed description of the CIF data dictionaries. The final part of the book describes applications of CIFs, including some Fortran and ANSI C programs, which are also included on the accompanying CD-ROM. This final section may become dated quite soon, but the formal definitions, which make up most of the book, should be important for years to come.

This book is an essential reference for crystallographers, and for everyone who needs to check precisely what is recorded in a crystallographic information file. Future scientists will depend on these definitions, and so the time and effort devoted to the production of this book has been used well. Readers seeking a quick introduction to the CIF format may do better to consult the original paper (Acta Cryst. 1991, A47, 655-685), which outlines the structures of the files. However, everyone who needs a complete and authoritative description of the format, needs this book.

A successor to SwaN-MR - and MacOS X counterpart to MestReC windows program.

Public access to academic libraries
Does electronic access to journals restrict access for visitors? When journals were all printed, it was possible to go to libraries and read them. Electronic access has reduced this walk-up access, but not removed it. Many publishers allow walk-up access to their electronic journals as part of their license agreements, although access may be restricted, and libraries do not always make it possible to take advantage of the license terms.

Royal Society launches trial of new open access journal service
The Royal Society has started a trial of an open access journal service, called EXiS Open Choice (FAQ). This complements the Royal Society's existing journals. Authors now have the option to pay a fee to have their article available to everybody, as well as published in the existing journals. The first paper published in this way has had the publication fee paid by the Wellcome Trust. Royal Society's view on open access is available, as well as a detailed description of content availability for each journal.

The difference between MedLine and PubMed
MEDLINE (Medical Literature Analysis and Retrieval System Online) is the U.S. National Library of Medicine's main bibliographic database with references to journal articles in biomedicine and the life sciences. This is the main component of PubMed, which provides access to MEDLINE and some other resources, including articles published in MEDLINE journals which are beyond the scope of MEDLINE, such as general chemistry articles.

Public Library of Science [PLoS] losing money
Nature reports that the Public Library of Science is losing money. Its publishing model has just been adjusted to raise more money by charging authors more per article.

Top 500 computers
The list of the world's top 500 computers has been updated. First position goes to IBM's BlueGene, which is used for quantum chemistry and molecular dynamics, amongst other things. Since December 2005 (Chem. Inf. Lett. 2005, 11, #6, 69) the UK's top entry has moved up to number thirty (atomic weapons research), and the HPCx (UK national supercomputer service) has dropped to fifty-nine.

The difficulty of citation tracking
This article (abstract) shows how major databases give inconsistent results for citations. This is partly because of differing treatment of accents and punctuation and partly because of mistakes in the databases. However, the main reason is the different policies of the database companies in deciding what constitutes a valid reference. Analysing citations sounds as if it should be easy, but is much harder than it first appears.

Data preservation
The preservation of digital data is a headache for modern historians.

Cambridge MedChem Consulting
This company, run by Chris Swain provides medicinal chemistry consulting services, and links to resources, including iBabel, a Mac OS X graphical interface to Open Babel, which interconverts chemical structure formats.

Historical pigments
The Pigmentum Project is a programme to catalogue data on historical pigments. The Pigment Compendium is a reference work on the historical terminology and optical microscopy of pigments, which is also available as a searchable database.

BBC open news archive
The BBC is opening a section of its news archives as an experiment. There are terms and conditions for using them, but the BBC says, "You are welcome to download the clips, watch them, and use them to create something unique."

© 2006 J M Goodman, Cambridge
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