© s.j. coles 2006 ecrystals: a route for open access to small molecule crystal structure data simon...
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© S.J. Coles 2006
eCrystals: A Route for Open Access to Small Molecule Crystal Structure Data
Simon Coles
School of Chemistry,
University of Southampton, U.K.
© S.J. Coles 2006
The Data Overload Problem
Cl
Cl
Cl
Cl
Cl
Cl
ClCl Cl
Cl
Cl
ClCl
O
O
O
O
N
N
N
N
N+
O
O
O
N+
O
O
O
30,000,000
1.5,000,000
450,000
© S.J. Coles 2006
Funding Body Viewpoint
© S.J. Coles 2006
Open Access as the Answer?
• Open Access Journals • Author Self-Archiving
© S.J. Coles 2006
Separating Data from Interpretations
Underlying data
Intellect & Interpretation
© S.J. Coles 2006
Workflow Capture and Analysis
RAW DATA DERIVED DATA RESULTS DATA
© S.J. Coles 2006
The eCrystals Data Archive
http://ecrystals.chem.soton.ac.uk
© S.J. Coles 2006
Access to the underlying data
© S.J. Coles 2006
Metadata Publication
• Using simple Dublin Core • Crystal structure• Title (Systematic IUPAC Name)• Authors• Affiliation• Creation Date
• Additional chemical information through Qualified Dublin Core• Empirical formula• International Chemical Identifier (InChI)• Compound Class & Keywords
• Specifies which ‘datasets’ are present in an entry
• DOI http://dx.doi.org/10.1594/ecrystals.chem.soton.ac.uk/145
• Rights & Citation http://ecrystals.chem.soton.ac.uk/rights.html
• Application Profile http://www.ukoln.ac.uk/projects/ebank-uk/schemas/
© S.J. Coles 2006
Metadata and Data Quality Control Data manipulation toolbox
Associated Metadata
Value added
Format conversion
© S.J. Coles 2006
Harvesting & Aggregating: Google
Coles, S.J., Day, N.E., Murray-Rust, P., Rzepa, H.S., Zhang, Y., Org. Biomol. Chem., 2005, (10),1832-1834. DOI: 10.1039/b502828k
© S.J. Coles 2006
Harvesting: OAIster
© S.J. Coles 2006
Linking and aggregating
© S.J. Coles 2006
Embedded in a science portal
© S.J. Coles 2006
eBank/eCrystals Future
• Full embedding in daily laboratory practice• Roll out to other institutions• Full support from host institution• Community acceptance• Federation of repositories• Specialised aggregator services (Crystallography)• Generic aggregator services (Chemistry / Science)
© S.J. Coles 2006
Aggregator services
Institutional data repositoriesValidation
Deposit
Publishers: peer-review journals, conference proceedings, etc
Publication
Validation
Data analysis, transformation, mining, modelling
Search, harvest
Presentation services / portals
Data discovery, linking, citation
Laboratory repositoryDeposit
The eCrystals ‘Global’ Model
© S.J. Coles 2006
eCrystals in Education
• Component of MChem course
Devise Search Discover
ManipulateAnalyse
Compare
© S.J. Coles 2006
eCrystals in Education
• Popular compounds site
© S.J. Coles 2006
eCrystals in Education
• eMalaria Schools Project
© S.J. Coles 2006
eCrystals in Education
• eMalaria Schools Project