UKOLN is supported by: Developing e-Infrastructure to support new research and learning paradigms. Dr Liz Lyon, Director UKOLN, University of Bath, UK.
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UKOLN is supported by:
Developing e-Infrastructure to support new research and learning paradigms.
Dr Liz Lyon, DirectorUKOLN, University of Bath, UK
Building the Info Grid, Copenhagen, September 2005.
www.bath.ac.uk
a centre of expertise in digital information management
www.ukoln.ac.uk
DEFF Seminar, Copenhagen, September 2005
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Overview
1. e-Research: a changing landscape
2. Developing infrastructure: repository services & adding value• Aggregation and linking: eBank UK• Integration and workflows
3. Looking to the longer term: digital curation and preservation
1. e-Research: a changing landscape
DEFF Seminar, Copenhagen, September 2005
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Data Overload!
How do we disseminate?
EPSRC National Crystallography
Service
eScience - the data deluge
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Diversity of data collections• Very large, relatively homogeneous: Large-scale Hadron
Collider (LHC) outputs from CERN• Smaller, heterogeneous and richer collections: World Data Centre for
Solar-terrestrial Physics CCLRC• Small-scale laboratory results: “jumping robots” project
at the University of Bath• Population survey data: UK Biobank
• Highly sensitive, personal data: patient care records
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Taxonomy of data collections• Research collections:
jumping robots • Community collections:
Flybase at Indiana (with UC Berkeley )
• Reference collections: Protein Data Bank
Source: NSF Long-Lived Digital Data Collections
Draft report revised May 2005
Evolution……
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Experience of data-sharing
• Large scale data sharing in the life sciences Draft Report June 2005 Sponsored by UK research funding bodies MRC, BBSRC, NERC, JISC, Wellcome
• Outcomes & recommendations– Importance of standards and good quality metadata– Require a data management plan– Work needed on vocabularies & ontologies– Awareness of archiving & long term preservation
• Position of research funders and policy makers?
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DEFF Seminar, Copenhagen, September 2005
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Learning & Teaching workflows
Research & e-Science 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
Harvestingmetadata
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
The scholarly knowledge cycle.
Liz Lyon, Ariadne, July 2003.
This work is licensed under a Creative Commons LicenseAttribution-ShareAlike 2.0
© Liz Lyon (UKOLN, University of Bath), 2005
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A view in 2005
• Institutional repositories: country update CNI/JISC/SURF
• D-Lib Magazine September 2005• Emerging trends
– Germany 103, UK 31, Sweden 25– Policy: Germany YES, UK RCUK draft– National programmes: UK, Germany, Australia,
Sweden, Netherlands YES– Services: indexing, search, harvesting
2. Developing infrastructure: repository services & adding value
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Developing models• The e-Framework for Education & Research• JISC, UK and Department of Education, Science
& Training, Australia • www.e-framework.org
“The primary goal of the initiative is to produce an evolving and sustainable, open standards based service oriented technical framework to support the education and research communities.”
• Reference models• Service definitions
JISC-fundedcontent providers
institutionalcontent providers
externalcontent providers
brokers aggregators catalogues indexes
institutionalportals
subjectportals
learning managementsystems
media-specificportals
end-userdesktop/browser pr
esen
tatio
n
fusion
prov
isio
n
OpenURLlink servers
shared infrastructure
authentication/authorisation (Athens)
institutional profilingservices
terminology services
service registries
identifier services
metadata schema registries
© Andy Powell (UKOLN, University of Bath), 2005
This work is licensed under a Creative Commons LicenseAttribution-ShareAlike 2.0
JISC Information Environment architecture
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Learning & Teaching workflows
Research & e-Science workflows
Aggregator services:
eBank UK
Repositories : institutional, e-prints, subject, data, learning objects
Institutional presentation services: portals, Learning Management Systems, u/g, p/g courses, modules
Harvestingmetadata
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
DEFF Seminar, Copenhagen, September 2005
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eBank UK Project
• Two key themes:– Open access to datasets– Linking research data to publications and to learning
• JISC-funded from September 2003: now in Phase 2 • UKOLN at the University of Bath (lead), University of
Southampton, University of Manchester• Exemplar: e-Science testbed ‘Combechem’
– Grid-enabled combinatorial chemistry / crystallography– National Crystallography Service
• Resource Discovery Network / PSIgate physical sciences portal
• http://www.ukoln.ac.uk/projects/ebank-uk/
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The “hybrid” project team
• UKOLN• Michael Day• Monica Duke• Rachel Heery• Traugott Koch • Liz Lyon• +• Andy Powell
• Southampton• Les Carr• Simon Coles• Jeremy Frey• Chris Gutteridge• Mike Hursthouse• Andrew Milstead
• Manchester• John Blunden-Ellis
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Data Flow in eBank UK
Submit
Store/link
Data files
Metadata
Present
HTML
Institutional repository eCrystals
OA
I-P
MH
Harvest (XML)
Index and Search
Present
HTML
eBank aggregator service
Create
Deposition Interface
Local archive search
interface
Service Provider interfaces e.g. Subject PortalDeposit
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CombeChem: An EPSRC pilot project
X-Raye-Lab
Analysis
Properties
Propertiese-Lab
SimulationVideo
Diff
ract
omet
er
Grid Middleware
StructuresDatabase
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Crystallography workflowRAW DATA DERIVED DATA RESULTS DATA
• Initialisation: mount new sample set up data collection• Collection: collect data• Processing: process and correct images• Solution: solve structures• Refinement: refine structure• CIF: produce CIF (Crystallographic Information File)• Validation: chemical & crystallographic checks• Report: generate Crystal Structure Report
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DEFF Seminar, Copenhagen, September 2005
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A data repository entry
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Access to the underlying data: complex objects
ecrystals.chem.soton.ac.uk
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Harvesting: OAIster
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Aggregating: search & discover
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Linking data to publications
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eBank embedded in a science portal
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Ontologies for discovery in an interdisciplinary world
• Transform the ‘list’ into an ‘ontology’
• Embed ontology into the deposition process
• Publish keywords in OAI
• Aggregators use keywords for linking with the broader literature
• Researchers use keyword ontology in search and discovery services
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Persistent identifiers for data citation
• eBank use cases: depositor, author, service provider, reader, publisher, ?
• Schemes: DOI, Handle, ARK, PURL• Global identification: express as http URIs• Added value services: CrossRef, resolution
service, integration (Globus), look-up service, ?• Degree of trust or persistence• Costs• Future potential: political, ?• Domain identifiers: International Chemical Identifier
(InChI) codes
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Publication & citation of scientific primary data project
• National Library for Science & Technology (TIB), University of Hanover, Germany
• STD-DOI Project http://www.std-doi.de • DOI registry for datasets• Data requirements: quality control, long-term curation,
use DOI resolver• Data publication agents: World Data Center Climate,
GeoForschungsZentrum Potsdam• Exemplar data citation:
– Kamm, H; Machon, L; Donner, S (2004): Gas chromatography (KTB Field Lab), GFZ Potsdam. doi:10.1594/GFZ/ICDP/KTB/ktb-geoch-gaschr-p
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Integration into crystallographic publishing practices
Publishers seal of approval
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Integration into chemistry research workflows
• R4L Repository for the Laboratory Project (JISC-funded) automated data capture from instrumentation, registration of results
• SMART TEA electronic Laboratory notebook + annotations
• Related sub-domains of chemistry: SPECTRa Project (JISC-funded)• Research assessment (RAE) process?
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Integration into the curriculum and e-Learning workflows
• MChem course • Assess role in
Undergraduate Chemical Informatics courses
• Pedagogic evaluation• Introducing school
children to e-Research?
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Knowledge extraction & “post-processing”
New information & knowledge ………
• Mining (data, text, structures)
• Modelling (economic, climate, mathematical, bio)
• Analysis (statistical, lexical, pattern matching, gene)
• Presentation (visualisation, rendering)
• In federated repositories: Digital libraries, datasets, learning materials• Role of Google????
3. Looking to the longer term: digital curation & preservation
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For later use? In use now (and the future)?
Repositories and digital curation
Data preservation Data curation
Static Dynamic
“maintaining and adding value to a trusted body of digital information for current and future use”
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Assuring long term access to the research record• Trusted digital repositories
– Audit Checklist for Certification Draft Report– Research Libraries Group, August 2005– RLG-NARA Taskforce– Defined criteria under 4 categories
• Organisation
• Functions, processes & procedures
• Designated community & usability
• Technologies & technical infrastructure
• UK Digital Curation Centre http://www.dcc.ac.uk – 1st International DCC Conference Sep 29-30, Bath UK
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Thank you.Questions?…..
More information: UKOLN http://www.ukoln.ac.uk/
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