DOI and eScience Dr Anne E Trefethen Oxford

A Definition of e-Science ‘e-Science is about global collaboration in key areas of science,

my. Grid: Directly Supporting the e-Scientist my. Grid slides courtesy of Carole Goble Partners

(courtesy of Carole Goble, Manchester) my. Grid Project • Imminent ‘deluge’ of genomics data

An in silico experiment = a web of interconnected information and components People Provenance

The e. Bank Project • Building links between e-research data, from the Combe. Chem

(e. Bank slides courtesy of Liz Lyon and Jeremy Frey) Comb-e-Chem Project Video Simulation

Goals of e-Bank Project • Provide self archive of results plus the raw and

Crystallographic e-Prints Ø Direct Access to Raw Data from scientific papers Raw data sets

e-Bank: Some Comments • Data as well as traditional bibliographic information is made available

Virtual Learning Environment Undergraduate Students Digital Library E-Scientists Reprints Peer. Reviewed Journal & Conference

Data Publishing Databases, notably in biology, are replacing (paper) publications as a medium of

This is where DOI comes in… • • DOI use for publications, papers, talks

DOI Registration Agency for Scientific Data • May 2005 – New DOI Registration Agency

DOI in e-Bank • Are creating DOI for all data from a crystal structure

Notes • e. Bank/e. Crystals uses a full schema to describe the metadata, the

Some issues… • Issue of DOI via TIB (in Germany) • Cost of DOI

Conclusions • Publication of data and “paper” becoming integrated in the digital scholarly research

Acknowledgements With special thanks to Jeremy Frey, Andrew Milsted, Liz Lyon, Carole Goble IATUL

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DOI and e-Science Dr Anne E Trefethen Oxford e-Research Centre Anne. Trefethen@oerc. ox. ac. uk IATUL Porto, May 21, 2006

A Definition of e-Science ‘e-Science is about global collaboration in key areas of science, and the next generation of infrastructure that will enable it. ’ John Taylor Director General of Research Councils Office of Science and Technology, 2001 IATUL Porto, May 21, 2006

my. Grid: Directly Supporting the e-Scientist my. Grid slides courtesy of Carole Goble Partners Manchester, EBI, Southampton, Nottingham, Newcastle, Sheffield Astra. Zeneca Glaxo. Smith. Kline IBM Merck KGa. A SUN Microsystems Epistemics Ltd Genetic. Xchange Network Inference http: //mygrid. man. ac. uk IATUL Porto, May 21, 2006

(courtesy of Carole Goble, Manchester) my. Grid Project • Imminent ‘deluge’ of genomics data • Highly heterogeneous • Highly complex and inter-related • Convergence of data and literature archives IATUL Porto, May 21, 2006

An in silico experiment = a web of interconnected information and components People Provenance record of workflow runs Literature Provenance of the workflow template. Related workflows. Notes Data in and out Ontologies describing workflows IATUL Porto, May 21, 2006 Services used (courtesy of Carole Goble, Manchester)

The e. Bank Project • Building links between e-research data, from the Combe. Chem project, with scholarly communication and other on-line sources • Investigating the role of aggregator services in linking data -sets from Grid enabled projects to open data archives contained in digital repositories through to peer-reviewed articles as resources in portals • JISC-funded project led by UKOLN in partnership with the Universities of Southampton and Manchester (e. Bank slides courtesy of Liz Lyon and Jeremy Frey) IATUL Porto, May 21, 2006

(e. Bank slides courtesy of Liz Lyon and Jeremy Frey) Comb-e-Chem Project Video Simulation Diffractometer Properties Analysis Structures Database X-Ray e-Lab Properties e-Lab Grid Middleware IATUL Porto, May 21, 2006

Goals of e-Bank Project • Provide self archive of results plus the raw and analysed data • Links from traditionally published work provides the provenance to the work • Disseminate for “Public Review” – raw data provided so that users can check themselves • Avoid the “publication bottleneck” but still provide the quality check (e. Bank slides courtesy of Liz Lyon and Jeremy Frey) IATUL Porto, May 21, 2006

Crystallographic e-Prints Ø Direct Access to Raw Data from scientific papers Raw data sets can be very large and these are stored at National Datastore using SRB server (e. Bank slides courtesy of Liz Lyon and Jeremy Frey) IATUL Porto, May 21, 2006

e-Bank: Some Comments • Data as well as traditional bibliographic information is made available • Can construct high level search on data – aggregate data from many e-print systems • Build new data services • Will extend to provision of real spectra - rather than very reduced summaries - for chemistry publications (e. Bank slides courtesy of Liz Lyon and Jeremy Frey) IATUL Porto, May 21, 2006

Virtual Learning Environment Undergraduate Students Digital Library E-Scientists Reprints Peer. Reviewed Journal & Conference Papers Grid Technical Reports Preprints & Metadata E-Experimentation Publisher Holdings Graduate Students Institutional Archive IATUL Porto, May 21, 2006 Local Web Certified Experimental Results & Analyses Data, Metadata & Ontologies 5 Entire E-Science Cycle Encompassing experimentation, analysis, publication, research, learning (e. Bank slides courtesy of Liz Lyon)

Data Publishing Databases, notably in biology, are replacing (paper) publications as a medium of communication – Built and maintained with a great deal of human effort – Often do not contain source experimental data, sometimes just annotation/metadata – Borrow extensively from, and refer to, other databases – Researchers are now judged by databases as well as (paper) publications – Upwards of 1000 (public databases) in genetics • Integration of literature and data analysis of increasing importance - linking bio-database to literature, using publishers to check, complete or complement contents of such databases IATUL Porto, May 21, 2006

This is where DOI comes in… • • DOI use for publications, papers, talks etc Now also for Data Enables reference, citation of the data, data sets Enables ready tracking of use of data (Possibly for RAE!) • Need to think carefully about granularity of citation and DOI IATUL Porto, May 21, 2006

DOI Registration Agency for Scientific Data • May 2005 – New DOI Registration Agency appointed • TIB – The Technische Informationsbibliothek – German’s National Library of Science and Technology. IATUL Porto, May 21, 2006

DOI in e-Bank • Are creating DOI for all data from a crystal structure determination or DOIs for all separate files from each stag of the structure determination • DOI points to e-bank web page ie the data set surrounded by the metadata about the peopled and the material etc. Citation: Coles, S. J. , Hursthouse, M. B. , Frey, J. G. and Rousay, E. (2004), Southampton, UK, University of Southampton, Crystal Structure Report Archive. (doi: 10. 1594/ecrystals. chem. soton. ac. uk/145) IATUL Porto, May 21, 2006

IATUL Porto, May 21, 2006

Notes • e. Bank/e. Crystals uses a full schema to describe the metadata, the datasets, the relationships between the dataset and the separate files – this took many iterations between chemists and the digital library groups to refine its current structure. • German climate groups also using DOI and data IATUL Porto, May 21, 2006

Some issues… • Issue of DOI via TIB (in Germany) • Cost of DOI • Where does it point? Laboratory store? Institutional repository? National repository? • Global resolving vs community level? IATUL Porto, May 21, 2006

Conclusions • Publication of data and “paper” becoming integrated in the digital scholarly research cycle • DOI has a role to play • Still a lot to learn regarding optimal use • Have implicitly touched on Open Access but as policies begin to apply to data as well as publication research outputs, then the above will be even more so. IATUL Porto, May 21, 2006

Acknowledgements With special thanks to Jeremy Frey, Andrew Milsted, Liz Lyon, Carole Goble IATUL Porto, May 21, 2006