Crystallographic Information and Data Management

A Satellite Workshop to the 28th European Crystallographic Meeting

University of Warwick, Coventry, England
August 23-24, 2013

The CIF2/DDLm Workshop will take place at the University of Warwick on 23-24 August, 2013. Participation in the Workshop will be by invitation only, in order to permit close focus on technical aspects of dictionary design and extensions to the CIF syntax and dictionary methods. Individuals with a strong interest in these topics but who are not known to the Workshop organisers are, of course, welcome to apply for such an invitation. The main topics of the Workshop will be:

  • Introduction to the CIF2 extended syntax
  • Development of an API to permit community development of open-source libraries and tools
  • Introduction to DDLm, a dictionary definition language supporting algorithmic methods
  • Discussion of dREL, a prototyping methods evaluator language
  • Tutorials and demonstrations of JsCifBrowser, a CIF2 implementation in JavaScript
  • Approaches to CIF dictionary authoring

The development of the Crystallographic Information Framework (CIF) since the late 1980s has been supported by the International Union of Crystallography, by database organisations such as the Protein Data Bank and Cambridge Crystallographic Data Centre, and by active software developers in academia and industry. Many of the original developers are now at retirement age, and research support within Universities is more difficult to obtain, in part because of the interdisciplinary nature of the work. COMCIFS is looking to new ways to secure the long-term vitality of ongoing CIF dictionary and software development.

 Post-Workshop Symposium

The public Symposium at University of Warwick will celebrate the achievements of the CIF project in crystallographic publishing, databases and experimental data handling, and will look to the future as CIF and similar standards provide even more functionality to cope with the growing complexity of research data management. Structural crystallography as a discipline has had almost unrivalled success in promoting first-rate data and publication practices. More than a dozen experts will demonstrate the richness and effectiveness of existing best practice, and will set this in the context of a scientific research framework that places increasing emphasis on scientists' responsibilities for proper data handling.

The Symposium will attract attendees at the regional meeting of European Crystallographers. The programme is available at http://www.iucr.org/resources/cif/comcifs/symposium-2013

            

Programme

Day 1: Dictionaries

I. Current definition approaches

09:00-09:10 Welcome. Housekeeping arrangements and schedule B. McMahon
09:10-09:40 Writing ontologies for semantic physical science P. Murray-Rust
09:40-10:10 General principles for CIF definitions B. McMahon and S. R. Hall
10:10-10:30 Discipline considerations in writing CIF dictionaries I. D. Brown
10:30-10:50 Coffee
10:50-11:05 Successes and lessons from IUCr journals M. A. Hoyland
11:05-11:20 Successes and lessons from powder diffraction B. H. Toby
11:20-11:35 Successes and lessons from structural biology J. Westbrook
11:35-11:50 Successes and lessons from raw data management H. J. Bernstein
11:50-12:05 Recent developments at the Crystallography Open Database Saulius Gra┼żulis
12:05-13:00 Writing a layman's guide for dictionary construction. Collaborative exercise, facilitated by J. R. Hester
13:00-14:00 Lunch

II. DDLm definition approaches

14:00-14:30 New attributes for definitions in DDLm S. R. Hall and B. McMahon
14:30-15:00 Structural and conceptual changes using DDLm N. Spadaccini
15:00-15:30 Conversion of current core definitions to DDLm S. R. Hall and B. McMahon
15:30-16:00 Conversion of mmCIF/PDBx dictionary to DDLm J. Westbrook
16:00-16:30 Break

III. Taking CIF to  the wider scientific world

16:30-16:40 Preview of the Information and Data Management Symposium B. McMahon
16:40-16:50 Report on the CIF/NeXus/HDF5 meeting preceding this Workshop H.J. Bernstein
16:50-17:10 Namespace conventions and mixed-discipline data CIFs J. R. Hester
17:10-17:20 CIF2 syntax refresher J.C. Bollinger and J. R. Hester
17:20-18:00 General discussion on CIF2 and how to introduce next-generation dictionaries to existing workflows.

Day 2: Dictionary Applications

I. Software support for DDLm

09:00-09:30 Software for dictionary building and maintenance S.R. Hall and B. McMahon
09:30-10:30 DDLm methods for evaluation, definition and validation N. Spadaccini
10:30-11:00 Coffee
11:00-11:30 JsCifBrowser: a DDLm tool for CIF2 applications D. duBoulay and N. Spadaccini
11:30-13:00 Tutorial on the use of JsCifBrowser D. duBoulay and N. Spadaccini
13:00-14:00 Lunch

II. Designing and implementing an API for CIF

14:00-14:30 The Concrete Syntax Tree for dREL implemented in JsCifBrowser N. Spadaccini and D. duBoulay
14:30-15:00 Draft API specifications arising from the IUCr forum J.C. Bollinger
15:00-15:30 Round table on building future CIF APIs Facilitated by J.R. Hester, N. Spadaccini and J.C. Bollinger
15:30-16:00 Software licensing issues and documentation Discussion led by H.J. Bernstein, J.C. Bollinger and B. McMahon
16:00-16:30 Break
16:30-17:30 Where to from here: discussion on who does what and when?
17:15-18:00 COMCIFS business meeting
            

Sponsored by

COMCIFS, the IUCr Committee for the Maintenance of the CIF Standard
iucr
International Union of Crystallography
UWA
The University of Western Australia
wwPDB
Worldwide Protein Data Bank
ccdc
Cambridge Crystallographic Data Centre
ccdc
Digital Curation Centre
BL-Logo
The British Library
[CODATA logo]
CODATA
[Wiley logo]
Wiley
[Royal Society of Chemistry logo]

Royal Society of Chemistry

[Elsevier logo]
Elsevier

[ACS logo]
American Chemical Society

[Dectris logo]
DECTRIS

[Crystallography Open Database logo]

Crystallography Open Database,
supported by:

[Rigaku logo]
Rigaku

[Crystal Impact logo]

Crystal Impact

[Bruker logo]
Bruker

 

Date and venue

Friday/Saturday 23-24 August 2013

Room B2.02 Sciences Building
University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.