Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

report on the open meeting at Geneva

Dear Friends,

	I have appended below a report on the open COMCIFS meeting held
during the recent IUCr Congress in Geneva.  I have submitted this report
to the IUCr Newsletter.

			David Brown

Dr.I.David Brown,  Professor Emeritus
Brockhouse Institute for Materials Research,
McMaster University, Hamilton, Ontario, Canada
Tel: 1-(905)-525-9140 ext 24710
Fax: 1-(905)-521-2773

Report on the COMCIFS Open Meeting at the IUCr Congress in

     How to provide a seamless flow of computer-based information
between crystallography and its neighbouring disciplines was the
question discussed during the open COMCIFS meeting held during
the IUCr Congress in Geneva.  The talks addressed the need for
compatibility at two levels, firstly at the level of the
definition of scientific concepts and secondly at the level of
file structures .

     The session opened with a talk by Brian McMahon and ended
with a talk by John Westbrook, both of whom pointed out the need
for compatibility between the scientific definitions (the
ontologies) provided by the CIF (Crystallographic Information
File) dictionaries and those provided by the dictionaries of the
related disciplines of chemistry and biology.  The Protein Data
Bank has achieved a seamless connection with molecular biology by
ensuring that the neighbouring fields use STAR dictionaries that
are fully compatible with CIF.   On the other hand chemical
databases are still in an experimental state and there is a real
danger that a variety of different and mutually incompatible
dictionaries will be developed.  This would make it difficult to
transfer information cleanly from one chemical datafile to
another and would complicate the interchange of information
between chemical and crystallographic databases.

     The remaining three talks of the session were devoted to
compatibility at a the level of the file structures.  While CIF
has the best developed set of dictionaries of any discipline, it
is currently not well provided with the software needed to
manipulate the files.  For this reason,  disciplines now starting
to develop file structures are attracted by the more recently
developed XML (eXtended Markup Language) because it is well
provided with software written by the information technology
community.  On the other hand, few if any disciplines have yet
developed the dictionaries needed for serious XML applications.
Both John Westbrook and Nick Spadaccini described programs that
can convert CIFs to XML files thereby allowing crystallographers
to exploit the XML software, but in a light-hearted presentation
Herbert Bernstein showed that although CIF and XML have many
similarities, there is more than one way in which a CIF can be
mapped into XML.  Emphasizing that CIF has always remained one
step ahead of XML in functionality, Syd Hall demonstrated an
advanced dictionary language, StarDDL (Star Dictionary Definition
Language), that will allow derived information to be calculated
directly using algorithms stored in the dictionary, a feature not
currently being considered for XML.  Because of the stable yet
flexible design of CIF, the large archive of CIFs built up over
the last decade will be able to exploit this feature, allowing
the user to retrieve derived information that may not be
explicitly stored in the CIF.

     The session gave the impression of a field expanding so
rapidly that, even though software and dictionary developments
may have difficulty keeping up with each other, the CIF project
remains on the cutting edge of information technology and the
opportunities for developing innovative software have never been

David Brown

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Science Council (admitted 1947). Member of CODATA, the ISC Committee on Data. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

International Science Council Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.