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Report of IUCr Representative to CODATA 2004-2006

CODATA requires a report on activities from each member organization
for presentation to its General Assembly (this will take place in Beijing
in late October). For your interest I append a copy of the report I have
just sent to CODATA. I have also transmitted the formal IUCr response to the
GICSI prospectus.

Best wishes


                           Report to CODATA
                         of Activities of the
               International Union of Crystallography (IUCr)

The International Union of Crystallography (IUCr) is a scientific union
adhering to the International Council for Science (ICSU). Its objectives
are to promote international cooperation in crystallography and to
contribute to all aspects of crystallography, to promote international
publication of crystallographic research, to facilitate standardization
of methods, units, nomenclatures and symbols, and to form a focus for
the relations of crystallography to other sciences.

Crystallographic Databases
Several independent databases exist that store and manage the results of
crystal structure determinations and other non-structural data. Among the
most important are 
 - the Cambridge Structural Database for organic and metal-organic
   small-molecule structures and oligonucleotides (CSD)
 - the Worldwide Protein Data Bank for protein and nucleic acid structures
   (PDB) (http://www.wwpdb.org/) - this federation now includes the RCSB
   Protein Data Bank in the United States, the European Bioinformatics
   Institute MSD, the Japanese PDBj and BioMagResBank in the US;
 - the Inorganic Crystal Structure Database for inorganic materials (ICSD)
 - the Metals Crystallographic Data File for metals (CRYSTMET)
 - the Powder Diffraction File (http://www.icsd.com).

These databases are curated by independent organisations, but the IUCr
monitors their development through a standing Database Committee (CCD) that
reports directly to the Union's Executive Committee.

Data Exchange
Development continues on the Crystallographic Information File (CIF), the
standard file format for archiving and exchanging crystallographic data.
Continual updates are made as required to the data dictionaries defining
specific items in the areas of small-molecule structural
crystallography (coreCIF), macromolecular structures (mmCIF), powder
diffraction (pdCIF), precision electron density studies (rhoCIF),
crystallographic symmetry (symCIF), modulated structures (msCIF), and
image-plate data, annotation and analysis (imgCIF).  Reviews of the CIF
project were presented at an open meeting during the IUCr Congress in
Florence, Italy, during August 2005. A successful workshop in Honolulu,
Hawaii, in August 2006 undertook to establish imgCIF as a standard
self-documenting format for synchrotron image data at large facilities.

Work continues between the IUCr and the RCSB Protein Data Bank to
streamline deposition and publication of macromolecular structures through
development of required CIF data items for journal publication.  The IUCr
has developed a CIF editor (publCIF) aimed at authors of small-molecule
structure reports that allows easy creation and modification of CIF-based
journal articles.

A new-generation dictionary definition language is under active development
that will increase automated handling and validation of the attributes of CIF
data sets.

The complete CIF specification and data dictionaries are described in
International Tables for Crystallography Volume G: Definition and Exchange
of Crystallographic Data (2005), edited by S. R. Hall and B. McMahon
(Dordrecht: Springer; http://it.iucr.org/g).

Data Validation
All structural data sets published in IUCr journals have since 1990 been
checked for internal consistency by software capable of reading CIF
submission or deposit files directly. The checking procedures are published
on the web, and a public service to return a standard report on structures
subjected to these checks has been established at http://checkcif.iucr.org.
This service continues to function as a community standard for reviewing and
assessing the consistency and quality of small-molecule and inorganic
structure determinations.

Electronic Publishing
The IUCr publishes seven primary research journals in crystallography, and
a seventh covering the technology, instrumentation and uses of synchrotron
radiation. The most recent, online-only, journal, Structural Biology and
Crystallization Communications, was launched in 2005, and includes
macromolecular structure determinations. The experimental data sets
associated with articles in these journals are freely available for
download as supplementary files; access to them is not restricted to
journal subscribers.

The IUCr's programme of Data Exchange, Quality Assurance and Integrated
Data Publication (CIF and checkCIF) was recognised by the 2006 Award
for Publishing Innovation of the Association of Learned and Professional
Society Publishers (ALPSP).

The IUCr continues to collaborate with the Cambridge Crystallographic
Data Centre and the Inorganic Crystal Structure Database to check new
submissions for prior publication.

A major project during the past two years has been the digitisation of the
book series International Tables for Crystallography, which includes
many reference data tables. The online edition is available from

Open Access to Crystallographic Data
Collaboration continues between the IUCr and a number of service
crystallography facilities who are working with national scientific
computing grid funding agencies to collect and store data sets. The IUCr
has helped to specify metadata allowing structured querying and retrieval
of data sets, in order to develop an infrastructure suitable for
centralised harvesting or archiving of crystallographic data in
subject-specific repositories.

The IUCr has considered the initial prospectus for a multi-stakeholder
Global Information Commons for Science Initiative (GICSI), and has prepared
a formal statement for submission by its Representatives to CODATA and the
International Council for Scientific and Technical Information (ICSTI). The
response, available at http://www.iucr.org/iucr-top/iucr/gicsi/, details
the IUCr's own actions to support such a global commons, but emphasises the
need for sustainability in such initiatives and the danger of undermining
existing service-providing data organizations.

Brian McMahon

27 September 2006

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