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© S.J. Coles 2006 Usability WS, NeSC Jan 06 Enabling the reusability of scientific data: Experiences with designing an open access infrastructure for sharing.

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Presentation on theme: "© S.J. Coles 2006 Usability WS, NeSC Jan 06 Enabling the reusability of scientific data: Experiences with designing an open access infrastructure for sharing."— Presentation transcript:

1 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Enabling the reusability of scientific data: Experiences with designing an open access infrastructure for sharing datasets Simon J. Coles EPSRC National Crystallography Service School of Chemistry University of Southampton

2 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Data & the Publication Problem 25,000,000 2,000, ,000

3 © S.J. Coles 2006 Usability WS, NeSC Jan 06 A Different Approach to Data Publication? Underlying dataIntellect & Interpretation

4 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Requirements Capture of all digital data and information generated during the course of an experiment Data validation Adding value Archival system for data with attached bibliographic and chemical metadata Automatic report generation Schema and protocols for publication and dissemination of a dataset

5 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Open Access Crystal Structure Archive ecrystals.chem.soton.ac.uk

6 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Access to the Underlying Data

7 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Publicising Content

8 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Harvesting, Linking and Aggregating

9 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Usability: Quality & Uniformity of data Different laboratories, practices & instruments present a heterogeneous body of data Publish according to IUCr ratified schema To support publication according to this schema a toolbox add-on to the archive has been developed Toolbox requires 2 mandatory files only & is capable of performing file format conversions and generate value added files

10 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Usability: Ease of Deposition & Metadata Quality Minimal number of manual metadata entries – many can be hardwired into the system Deposition guidelines initially prepared by students to provide impartial feedback Full documentation and in-line help/examples Restrained lists, e.g. Keywords Data deposited automatically by toolbox Automated generation of metadata for report and OAI interface

11 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Usability: Data Validation Peer review removed from self deposit publication Simple checks for consistency made by the toolbox Checks for crystallographic integrity made through a web service (IUCr, CHECKCIF) Introduction of data editor for the archive; a deposition must be signed-off by a recognised professional before going live Quality indicators automatically taken from dataset and presented in HTML jump-off page

12 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Usability: Identifiers URL of deposited dataset provides an identifier Persistent only if the Institutional support model is accepted / adopted Signed-up to an agency to register metadata relating to datasets with a DOI Pay registry to ensure that DOI always resolves to associated dataset (10cents to register 1cent per annum to maintain) InChI chemical identifier - a unique text descriptor for a molecule

13 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Usability: Dissemination & Aggregation OAI metadata schema; ratified by IUCr & chemical community OAI covers bibliographic terms; must introduce chemical terms Both library and subject specific aggregators satisfied Chemical linking; InChI, chemical classifications and restricted keywords list

14 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Usability: Endorsement Feedback during development from technical publishing arm of IUCr Designed for automatic incorporation into CSD (global database operated by CCDC) Accepted by Executive Committee of IUCr Reuse of data achieved in collaboration with Leverhulme Centre for Molecular Informatics

15 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Usability: Community Uptake Southampton archive about to publish routinely via the archive Five crystallography laboratories in UK agreed to adopt philosophy, install and populate archives CCDC will harvest required data from all archives IUCr will harvest and curate all data Develop aggregator services in collaboration with IUCr

16 © S.J. Coles 2006 Usability WS, NeSC Jan 06 Usability: The Next Challenges Full acceptance by chemical community –Validation worries –Curation worries –The requirement for as many peer reviewed publications as possible (despite quality) Full acceptance by wider chemistry publishing community –Loss of control over underlying data –Faith in Open Archives replacing experimental descriptions in articles Development of fully functional aggregator services


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