UKOLN is supported by: Enhancing access to research data: the challenge of crystallography Rachel Heery, Monica Duke, Michael Day UKOLN, University of Bath Leslie Carr, Simon Coles University of Southampton www.bath.ac.u k A centre of expertise in digital informaion management JCDL 2005, June 7-11, Denver
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UKOLN is supported by: Enhancing access to research data: the challenge of crystallography Rachel Heery, Monica Duke, Michael Day UKOLN, University of.
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UKOLN is supported by:
Enhancing access to research data: the challenge of crystallography
Rachel Heery, Monica Duke, Michael Day
UKOLN, University of Bath
Leslie Carr, Simon Coles
University of Southampton
www.bath.ac.uk
A centre of expertise in digital informaion management
JCDL 2005, June 7-11, Denver
Enhancing access to research data: overview
• Crystallography as an exemplar
• Impact of digital technologies on scientific research process
• Need new modes of data curation
• eBank project: applying digital library techniques to support data curation
• Next steps
Changes in scientific research process
• Increasing data volumes from eScience / Grid-enabled / cyber-infrastructure applications, “big science”
• Changing research methods: high througput technologies, automation, ‘smart labs’
• Potential for re-use of data, new inter-disciplinary research
• Different types of data: observational data, experimental data, computational data: different stewardship requirements
Data Overload!
How do we disseminate?
EPSRC National Crystallography
Service
The data deluge: crystallography
Data overload & the publication bottleneck
Cl
Cl
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Cl
Cl
Cl
ClCl Cl
Cl
Cl
ClCl
O
O
O
O
N
N
N
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N+
O
O
O
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O
O
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25,000,000
2,000,000
300,000
Current Publishing Process• Journal articles: aims, ideas, context, conclusions – only most significant data
• Raw & underlying data required by peers not readily available
Context: existing data repositories• National data archives:
– UK Data Archive, Arts and Humanities Data Service, US National Archives and Records Administration (NARA), Atlas Datastore
• Discipline specific archives: – GenBank, Protein Data Bank
• Crystallography archives– Cambridge Crystallographic Data Centre (Cambridge
Structural Database) , Indiana University Molecular Structure Center (Crystal Data Server, Reciprocal Net), FIZ Karlsruhe (Inorganic crystals), Toth Information Systems (CHRYSTMET)
• Journals require deposit of data to support articles– Typically deposit of summary data…. partial coverage
Crystallography workflowRAW DATA DERIVED DATA RESULTS DATA
• Initialisation: mount new sample on diffractometer & set up data collection
• Collection: collect data• Processing: process and correct images• Solution: solve structures• Refinement: refine structure• CIF: produce CIF (Crystallographic Information File)• Validation: chemical & crystallographic checks
eBank UK project overview
• JISC funded in 2003, now in Phase 2 to 2006• Joint effort between crystallographers, computer
scientists, digital library researchers• Investigating contribution of existing digital library
technologies to enable ‘publication at source’• Partners have interest in dissemination of
chemistry research data, open access, OAI, institutional repositories http://www.ukoln.ac.uk/projects/ebank-uk/
eBank project team
University of Bath, UKOLN• Michael Day, Monica Duke, Rachel Heery, Liz
Lyon, Traugott KochUniversity of Southampton, School of Chemistry• Simon Coles, Jeremy Frey, Mike HursthouseUniversity of Southampton, School of Electronics
and Computer Science• Leslie Carr, Chris GutteridgeUniversity of Manchester, PSIgate• John Blunden-Ellis
eBank phase one: achievements• Gathered requirements from crystallographers • Established pilot institutional repository for
crystallography data at Southampton with web interface
• Developed a demonstrator aggregator service at UKOLN (CCDC exploring aggregation service)
• Developed appropriate schema • Demonstrated a search interface as an embedded
service at PSIgate portal• Demonstrated an added value service linking