Presentation is loading. Please wait.

Presentation is loading. Please wait.

Federation eCrystals Federation: Open Repositories for Data-driven Science Dr Liz Lyon, UKOLN, University of Bath, UK Dr Simon Coles, University of Southampton,

Published byAnna Lancaster Modified over 11 years ago

Similar presentations

Presentation on theme: "Federation eCrystals Federation: Open Repositories for Data-driven Science Dr Liz Lyon, UKOLN, University of Bath, UK Dr Simon Coles, University of Southampton,"— Presentation transcript:

1 Federation eCrystals Federation: Open Repositories for Data-driven Science Dr Liz Lyon, UKOLN, University of Bath, UK Dr Simon Coles, University of Southampton, UK Chemical Informatics Workshop, Manchester, March 2008 This work is licensed under a Creative Commons Licence Attribution-ShareAlike 3.0 http://creativecommons.org/licenses/by-sa/3.0/

2 Themes 1.Context: Institutional data repositories crystallography exemplar 2.Scale: repository federations 3.Longevity: Digital curation and preservation 4.Integration: Semantic challenges

3 eBank Project – building the eCrystals Data Repository ePrints platform @ Southampton Institutional Repository exemplar Embedded in workflow http://ecrystals.chem.soton.ac.uk Started Sept 2003 Scholarly knowledge cycle context UKOLN-led interdisciplinary team

4 Scaling Up Report Phase 3 findings: Data policy should reflect lab practice & institutional model Diverse lab practice LIMS proprietary formats Data quality criteria/validation Prior publication problem We need automated assignment of terms for data discovery No discipline preservation model

5 nλ = 2 d sinθ The

6 eCrystals Repository ePrints.org v3.0

7 Repository Foundations 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 Application Profile http://www.ukoln.ac.uk/projects/ebank-uk/schemas/ DOI links http://dx.doi.org/10.1594/ecrystals.chem.soton.ac.uk/145 Rights & Citation http://ecrystals.chem.soton.ac.uk/rights.html Learned society + subject repository support

8 Federation interoperability & linking services Roll-out in 2 phases led by University of Southampton Establish Federation policies, application profile, mappings Bi-directional links with derived articles in publisher repositories, IUCr, Royal Society of Chemistry (RSC), Chemistry Central: scholarly knowledge cycle StOReLink project - Test linking options: StORe middleware and CLADDIER OAI-ORE Testbed eChemistry project

9 Laboratory practice & workflow Community standard CIF Mixed lab practice – central service facility versus single staff crystallographer in department Achieve end-to-end workflow Challenge of instrument manufacturers with proprietary formats Repository Lite for smaller lab operations? X-ray diffractometers

10 eBank-UK Phase 3 Curation & Preservation Study: Sustainability issues http://www.ukoln.ac.uk/projects/ebank- uk/curation/ Examined four main areas 1.Audit and certification (TRAC, DRAMBORA, NESTOR, ISO International repository audit and certification BOF Group) 2.The Open Archival Information System (OAIS) and Representation Information (RI) 3.eBank-UK application profile and preservation metadata 4.ePrints.org repository platform Recommendations: Self-assessment using DRAMBORA Consider Representation Information in wider context Develop preservation strategy Capture preservation metadata - PREMIS

11 Crystallographic schema underpins CIF (Crystallographic Information Framework), but is limited to data parameters e.g. cell_length_a Semantic issues

12 IUCr Acta Cryst 1992 Limited set of keywords describing methods, properties & applications, compounds, attributes No established crystallography dictionary or controlled vocabulary to give chemistry context

13 What do we want to do? Support depositors keyword/term assignment Facilitate and improve automated indexing Support advanced search / browse Allow metadata validation & enhancement Apply across a heterogeneous Federation Cross search, cross browse functionality Link data to all associated digital objects Develop domain semantics / vocabulary Use domain-specific authority files Mine to discover rather than find Achieve full inter-disciplinary integration

14 Some (semantic) issues….. How are terms assigned? Informal tags and/or structured KOS? How is a vocabulary curated and maintained? Can a vocabulary be transformed into a (Semantic Web related understanding) ontology? Disambiguation, acronyms, IUPAC names Persistent identification for data citation Granularity of data citation Data (and metadata) quality, provenance, validation Embedding within complex workflows Use collaborative social approaches? Community adoption: becomes part of the culture

15 Federation Questions? Slides will be available at : http://wiki.ecrystals.chem.soton.ac.uk/index.php http://wiki.ecrystals.chem.soton.ac.uk/index.php http://www.ukoln.ac.uk/ukoln/staff/e.j.lyon/presentations.html This work is licensed under a Creative Commons Licence Attribution-ShareAlike 3.0 http://creativecommons.org/licenses/by-sa/3.0/

Download ppt "Federation eCrystals Federation: Open Repositories for Data-driven Science Dr Liz Lyon, UKOLN, University of Bath, UK Dr Simon Coles, University of Southampton,"

Similar presentations

EPrints - Introducing EPrints 3 Software William J Nixon Digital Library Development Manager, University of Glasgow With many thanks to Les Carr and the.

EPrints - Introducing EPrints 3 Software William J Nixon Digital Library Development Manager, University of Glasgow With many thanks to Les Carr and the.
IATUL Porto, May 21, 2006 DOI and e-Science Dr Anne E Trefethen Oxford e-Research Centre

IATUL Porto, May 21, 2006 DOI and e-Science Dr Anne E Trefethen Oxford e-Research Centre
DRIVER Long Term Preservation for Enhanced Publications in the DRIVER Infrastructure 1 WePreserve Workshop, October 2008 Dale Peters, Scientific Technical.

DRIVER Long Term Preservation for Enhanced Publications in the DRIVER Infrastructure 1 WePreserve Workshop, October 2008 Dale Peters, Scientific Technical.
AHM, Nottingham, September 20041 eBank UK : linking research data, scholarly communication and learning. Dr Liz Lyon, UKOLN, University of Bath Dr Simon.

AHM, Nottingham, September eBank UK : linking research data, scholarly communication and learning. Dr Liz Lyon, UKOLN, University of Bath Dr Simon.
A centre of expertise in data curation and preservation DCC/NeSC eScience Workshop, June 2008 Working in partnership with the eScience community This work.

A centre of expertise in data curation and preservation DCC/NeSC eScience Workshop, June 2008 Working in partnership with the eScience community This work.
S.J. Coles a*, M.B. Hursthouse a, R.A. Stephenson a, P. Cliff b, E. Lyon b, M. Patel b J. Downing c & P. Murray-Rust.

S.J. Coles a*, M.B. Hursthouse a, R.A. Stephenson a, P. Cliff b, E. Lyon b, M. Patel b J. Downing c & P. Murray-Rust.
© S.J. Coles 2006 Usability WS, NeSC Jan 06 Enabling the reusability of scientific data: Experiences with designing an open access infrastructure for sharing.

© S.J. Coles 2006 Usability WS, NeSC Jan 06 Enabling the reusability of scientific data: Experiences with designing an open access infrastructure for sharing.
Opening the Research Data Lifecycle Workshop Capturing and Sharing Research Data Simon Coles School of Chemistry, University of Southampton, U.K.

Opening the Research Data Lifecycle Workshop Capturing and Sharing Research Data Simon Coles School of Chemistry, University of Southampton, U.K.
© S.J. Coles 2006 Digital Repositories as a Mechanism for the Capture, Management and Dissemination of Chemical Data Simon Coles School of Chemistry, University.

© S.J. Coles 2006 Digital Repositories as a Mechanism for the Capture, Management and Dissemination of Chemical Data Simon Coles School of Chemistry, University.
Linking Data and Publications: the Chemistry Way Simon Coles School of Chemistry, University of Southampton, U.K. CLADDIER workshop.

Linking Data and Publications: the Chemistry Way Simon Coles School of Chemistry, University of Southampton, U.K. CLADDIER workshop.
S.J. Coles a*, J.G. Frey a, M.B. Hursthouse a, L. Carr b & C.J. Gutteridge b. a School of Chemistry, University of Southampton, UK.; b School of Electronics.

S.J. Coles a*, J.G. Frey a, M.B. Hursthouse a, L. Carr b & C.J. Gutteridge b. a School of Chemistry, University of Southampton, UK.; b School of Electronics.
© S.J. Coles 2006 Digital Repositories as a Mechanism for the Capture, Management and Dissemination of Chemical Data Simon Coles School of Chemistry, University.

© S.J. Coles 2006 Digital Repositories as a Mechanism for the Capture, Management and Dissemination of Chemical Data Simon Coles School of Chemistry, University.
RCUK, Octiber 20041 Archiving research data and research publications. Dr Leslie Carr, Intelligence, Agents Multimedia, University of Southampton Dr Simon.

RCUK, Octiber Archiving research data and research publications. Dr Leslie Carr, Intelligence, Agents Multimedia, University of Southampton Dr Simon.
© S.J. Coles 2006 eCrystals: A Route for Open Access to Small Molecule Crystal Structure Data Simon Coles School of Chemistry, University of Southampton,

© S.J. Coles 2006 eCrystals: A Route for Open Access to Small Molecule Crystal Structure Data Simon Coles School of Chemistry, University of Southampton,
UKOLN is supported by: Enhanced support for eScience: the role of Digital Libraries Digital Libraries Go eScience, ECDL, Alicante September 2006 Rachel.

UKOLN is supported by: Enhanced support for eScience: the role of Digital Libraries Digital Libraries Go eScience, ECDL, Alicante September 2006 Rachel.
A centre of expertise in digital information management www.ukoln.ac.uk UKOLN is supported by: Digital libraries and digital scholarship: changing roles.

A centre of expertise in digital information management UKOLN is supported by: Digital libraries and digital scholarship: changing roles.
A centre of expertise in digital information management www.ukoln.ac.uk UKOLN is supported by: Adding Value to Data and Information: Moving towards a Science.

A centre of expertise in digital information management UKOLN is supported by: Adding Value to Data and Information: Moving towards a Science.
A centre of expertise in digital information management www.ukoln.ac.uk UKOLN is supported by: Dealing with Data: Perspectives on Progress to Date Dr Liz.

A centre of expertise in digital information management UKOLN is supported by: Dealing with Data: Perspectives on Progress to Date Dr Liz.
A centre of expertise in digital information management www.ukoln.ac.uk UKOLN is supported by: Dealing with Data: One Year On Dr Liz Lyon, Director, UKOLN,

A centre of expertise in digital information management UKOLN is supported by: Dealing with Data: One Year On Dr Liz Lyon, Director, UKOLN,
UKOLN is supported by: From research data to new knowledge: a lifecycle approach. Dr Liz Lyon, Director UKOLN, University of Bath, UK JISC/SURF/CNI Conference.

UKOLN is supported by: From research data to new knowledge: a lifecycle approach. Dr Liz Lyon, Director UKOLN, University of Bath, UK JISC/SURF/CNI Conference.

Similar presentations

Ads by Google