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AHM, Nottingham, September 20041 eBank UK : linking research data, scholarly communication and learning. Dr Liz Lyon, UKOLN, University of Bath Dr Simon.

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Presentation on theme: "AHM, Nottingham, September 20041 eBank UK : linking research data, scholarly communication and learning. Dr Liz Lyon, UKOLN, University of Bath Dr Simon."— Presentation transcript:

1 AHM, Nottingham, September eBank UK : linking research data, scholarly communication and learning. Dr Liz Lyon, UKOLN, University of Bath Dr Simon Coles, School of Chemistry, University of Southampton

2 AHM, Nottingham, September Overview In context: scholarly communications –Open Access –Data, information, workflows and provenance The data publication bottleneck –e-Science and crystallography –Comb-e-chem Project eBank UK –Information architecture and data flow –Interoperability issues Challenges for the future

3 Scholarly communications

4 AHM, Nottingham, September Current chemistry publishing protocols Ideas and interpretations Results & derived data Hooks into the literature Raw data!

5 AHM, Nottingham, September 20045

6 AHM, Nottingham, September 20046

7 AHM, Nottingham, September It is envisaged that the sharing of primary data would prevent unnecessary repetition of experiments and enable scientists to build directly on each others work, creating greater efficiencies and productivity in the research process. The government line

8 AHM, Nottingham, September Research & e-Science workflows Aggregator services: national, commercial Repositories : institutional, e-prints, subject, data, learning objects Data curation: databases & databanks Validation Harvesting metadata Data creation / capture / gathering: laboratory experiments, Grids, fieldwork, surveys, media Deposit / self- archiving Peer-reviewed publications: journals, conference proceedings Publication Validation Data analysis, transformation, mining, modelling Searching, harvesting, embedding Presentation services: subject, media-specific, data, commercial portals Resource discovery, linking, embedding Linking The scholarly knowledge cycle. Liz Lyon, eBankUK article. Ariadne, July 2003.

9 AHM, Nottingham, September Learning & Teaching workflows Aggregator services: national, commercial Repositories : institutional, e-prints, subject, data, learning objects Institutional presentation services: portals, Learning Management Systems, u/g, p/g courses, modules Harvesting metadata Resource discovery, linking, embedding Peer-reviewed publications: journals, conference proceedings Validation Resource discovery, linking, embedding Deposit / self- archiving Learning object creation, re-use Searching, harvesting, embedding Quality assurance bodies Validation Presentation services: subject, media-specific, data, commercial portals

10 AHM, Nottingham, September Learning & Teaching workflows Research & e-Science workflows Aggregator services: national, commercial Repositories : institutional, e-prints, subject, data, learning objects Data curation: databases & databanks Institutional presentation services: portals, Learning Management Systems, u/g, p/g courses, modules Validation Harvesting metadata Data creation / capture / gathering: laboratory experiments, Grids, fieldwork, surveys, media Resource discovery, linking, embedding Deposit / self- archiving Peer-reviewed publications: journals, conference proceedings Publication Validation Data analysis, transformation, mining, modelling Resource discovery, linking, embedding Deposit / self- archiving Learning object creation, re-use Searching, harvesting, embedding Quality assurance bodies Validation Presentation services: subject, media-specific, data, commercial portals Resource discovery, linking, embedding Linking

11 AHM, Nottingham, September Learning & Teaching workflows Research & e-Science workflows Aggregator services: eBank UK Repositories : institutional, e-prints, subject, data, learning objects Data curation: databases & databanks Institutional presentation services: portals, Learning Management Systems, u/g, p/g courses, modules Validation Harvesting metadata Data creation / capture / gathering: laboratory experiments, Grids, fieldwork, surveys, media Resource discovery, linking, embedding Deposit / self- archiving Peer-reviewed publications: journals, conference proceedings Publication Validation Data analysis, transformation, mining, modelling Resource discovery, linking, embedding Deposit / self- archiving Learning object creation, re-use Searching, harvesting, embedding Quality assurance bodies Validation Presentation services: subject, media-specific, data, commercial portals Resource discovery, linking, embedding Linking

12 The Data Publication Bottleneck

13 AHM, Nottingham, September Data Overload! How do we disseminate? EPSRC National Crystallography Service The data deluge

14 AHM, Nottingham, September CombeChem: An EPSRC pilot project X-Ray e-Lab Analysis Properties Properties e-Lab Simulation Video Diffractometer Grid Middleware Structures Database

15 AHM, Nottingham, September Grid E-Scientists Entire E-Science Cycle Encompassing experimentation, analysis, publication, research, learning 5 Institutional Archive Local Web Publisher Holdings Digital Library E-Scientists Graduate Students Undergraduate Students Virtual Learning Environment E-Experimentation E-Scientists Technical Reports Reprints Peer- Reviewed Journal & Conference Papers Preprints & Metadata Certified Experimental Results & Analyses Data, Metadata & Ontologies

16 The eBank UK Project

17 AHM, Nottingham, September eBank UK project JISC-funded for 1 year from September 2003 UKOLN at the University of Bath (lead), University of Southampton, University of Manchester Building the links between research data, scholarly communication and learning Exemplar: e-Science testbed Combechem –Grid-enabled combinatorial chemistry –Crystallography, laser and surface chemistry examples –Development of an e-Lab using pervasive computing technology –National Crystallography Service Resource Discovery Network / PSIgate physical sciences portal

18 AHM, Nottingham, September The project team UKOLN Michael Day Monica Duke Rachel Heery Liz Lyon + Andy Powell Southampton Les Carr Simon Coles Jeremy Frey Chris Gutteridge Mike Hursthouse Manchester John Blunden-Ellis

19 AHM, Nottingham, September First steps: establishing common ground… Understand the data creation process Terminology and definitions –Data –Metadata –Datafile –Dataset –Data holding Different views –Digital library researchers, computer scientists, chemists –Generic vs specific –Modeller vs practitioner Aim for a common ontology Modelling the domain Creating a metadata schema

20 AHM, Nottingham, September Progress update Version 2.0 eBank metadata schema Enhanced ePrints.org software Pilot institutional e-data repository for harvesting (raw, derived, results data) Exports records as ebank_dc and oai_dc Validation of schema Pilot eBank UK aggregator service Developing search interface Version 1.0 Testing with PSIgate physical sciences portal – embedding eBank UK

21 AHM, Nottingham, September Crystallography workflow 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 format) Report: generate Crystal Structure Report RAW DATADERIVED DATARESULTS DATA

22 AHM, Nottingham, September Deposition into the archive

23 AHM, Nottingham, September An Archive entry ecrystals.chem.soton.ac.uk For a demo come to the JISC booth! 13:00 & during tea

24 AHM, Nottingham, September All the way back to the underlying data…

25 AHM, Nottingham, September Some metadata issues Using simple and qualified Dublin Core Additional chemical information in schema for harvesting e.g. empirical formula Schema contains International Chemical Identifier (InChI) Links to all datasets associated with an experiment Links to individual datasets within an experiment Links to eprints (and other published literature) derived from the data Using vocabularies specific to crystallography Engaging the broader scientific community to ensure different schemas are compliant and standards can emerge

26 AHM, Nottingham, September ebank_dc record (XML) Crystal structure (data holding) Crystal structure report (HTML) Dataset Institutional repository Deposit Dataset dc:identifier dcterms:references Linking dc:type=CrystalStructure and/or Collection Model input Andy Powell, UKOLN. Eprint oai_dc record (XML) dcterms:isReferencedBy dc:type=Eprint and/or Text Data flow in eBank Eprint jump-off page (HTML) dc:identifier Eprint manifestation (e.g. PDF) Linking

27 AHM, Nottingham, September ebank_dc record (XML) Crystal structure (data holding) Crystal structure report (HTML) Dataset Institutional repository eBank UK aggregator service ePrint UK aggregator service Subject service Deposit Harvesting OAI-PMH ebank_dc Harvesting OAI-PMH oai_dc Dataset dc:identifier dcterms:references Linking dc:type=CrystalStructure and/or Collection Model input Andy Powell, UKOLN. Eprint oai_dc record (XML) dcterms:isReferencedBy dc:type=Eprint and/or Text Data flow in eBank Eprint jump-off page (HTML) dc:identifier Eprint manifestation (e.g. PDF) Linking

28 AHM, Nottingham, September ebank_dc record (XML) Crystal structure (data holding) Crystal structure report (HTML) Dataset Institutional repository eBank UK aggregator service ePrint UK aggregator service Subject service Deposit Harvesting OAI-PMH ebank_dc Harvesting OAI-PMH oai_dc Searching, linking and embedding Dataset dc:identifier dcterms:references Linking dc:type=CrystalStructure and/or Collection Model input Andy Powell, UKOLN. PSIgate portal Eprint oai_dc record (XML) dcterms:isReferencedBy dc:type=Eprint and/or Text Data flow in eBank Eprint jump-off page (HTML) dc:identifier Eprint manifestation (e.g. PDF) Linking

29 AHM, Nottingham, September Harvesting: OAIster

30 AHM, Nottingham, September Linking and aggregating: Search & discover For a demo come to the JISC booth! 13:00 & during tea or the buffet

31 AHM, Nottingham, September Linking and aggregating: Hit browsing

32 AHM, Nottingham, September And finally… eBank embedded in a science portal

33 AHM, Nottingham, September Currently we are…… Assessing outcomes of a Consultation Workshop held in August e.g. –Cost-benefit issues for researchers? –RAE / assessment impact? –Disciplinary differences? Presenting a demonstrator Completing supporting studies on (1) Provenance and (2) Data models and schema Promoting Open Access and Open eData Archives to international crystallographic organisations, publishers, learned societies Phase 2 proposal funding sought for further 12 months

34 Challenges for the future

35 AHM, Nottingham, September Phase 2 plan…….(1) Continue to progress towards generic metadata schemas Validation against other schema –CLRC Scientific Metadata Model Modify Eprints.org software to allow for more generic scientific data and schemas Metadata enhancement: subject keyword additions based on knowledge of keywords in related publications Investigate identifiers e.g. International Chemical Identifier (InChI code) Explore context sensitive linking: find me –Datasets by this person; Journal articles by this person; Datasets related to this subject; Journal articles on this subject; Learning objects by this person; Learning objects on this subject

36 AHM, Nottingham, September Phase 2…….(2) Full embedding into the crystallographic research and publishing communities Chemistry workflow embedding –SMART TEA e synthesis Lab –Other analytical techniques in chemistry e-Learning embedding and pedagogic evaluation –Undergraduate chemical informatics courses –Introduction to visiting schools Expand into other physical, mathematical, geological and engineering sciences Feasibility study in related domains – bio and medical sciences Feasibility study in unrelated domains – arts and humanities

37 Thank you. Questions?…..


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