Transcript eBank UK - linking research data, learning & scholarly

eBank UK : linking research data,
learning and scholarly communications.
Dr Liz Lyon, UKOLN, University of Bath
Dr Simon Coles, School of Chemistry, University of Southampton
JISC Joint Programmes Meeting 2005
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The wider context
Why create the e-Framework?
The JISC strategic context
Sarah Porter, 2005
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JISC-funded
content providers
institutional
content providers
external
content providers
authentication/authorisation (Athens)
service registries
metadata schema registries
brokers
aggregators
catalogues
indexes
identifier services
institutional profiling
services
OpenURL media-specific institutional
link servers
portals
portals
subject
portals
learning management
systems
terminology services
shared infrastructure
end-user
desktop/browser
© Andy Powell (UKOLN, University of Bath), 2005
This work is licensed under a Creative Commons License
Attribution-ShareAlike 2.0
JISC Information Environment architecture
Presentation services: subject, media-specific, data, commercial portals
Data creation /
capture /
gathering:
laboratory
experiments,
Grids,
fieldwork,
surveys, media
Resource
discovery, linking,
embedding
Data analysis,
transformation,
mining, modelling
Searching ,
harvesting,
embedding
Aggregator
services: national,
commercial
Resource
discovery,
linking,
embedding
Learning object
creation, re-use
Harvesting
metadata
Learning &
Teaching
workflows
Research &
e-Science
workflows
Repositories :
institutional,
e-prints, subject,
data, learning objects
Deposit / selfarchiving
Validation
Publication
Resource
discovery, linking,
embedding
The scholarly knowledge cycle.
Liz Lyon, Ariadne, July 2003.
© Liz Lyon (UKOLN, University of Bath), 2005
This work is licensed under a Creative Commons License
Attribution-ShareAlike 2.0
Deposit / selfarchiving
Institutional
presentation
services: portals,
Learning
Management
Systems, u/g, p/g
courses, modules
Peer-reviewed
publications: journals,
conference proceedings
JISC Joint Programmes Meeting 2005
Validation
Quality
assurance
bodies
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eScience - the data deluge
Data
Overload!
EPSRC National
Crystallography
Service
How do we
disseminate?
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Presentation services: subject, media-specific, data, commercial portals
Data creation /
capture /
gathering:
laboratory
experiments,
Grids,
fieldwork,
surveys, media
Resource
discovery, linking,
embedding
Data analysis,
transformation,
mining, modelling
Searching ,
harvesting,
embedding
Aggregator services:
eBank UK
Resource
discovery,
linking,
embedding
Learning object
creation, re-use
Harvesting
metadata
Research &
e-Science
workflows
Deposit / selfarchiving
Learning &
Teaching
workflows
Repositories :
institutional,
e-prints, subject,
data, learning objects
Validation
Publication
Deposit / selfarchiving
Institutional
presentation
services: portals,
Learning
Management
Systems, u/g, p/g
courses, modules
Resource
discovery, linking,
embedding
Peer-reviewed
publications: journals,
conference proceedings
JISC Joint Programmes Meeting 2005
Validation
Quality
assurance
bodies
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The eBank UK Project
eBank UK: background
• JISC-funded September 2003, Phase 2 February 2005
• UKOLN at the University of Bath (lead), University of
Southampton, University of Manchester
• Exemplar: e-Science testbed ‘Combechem’
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–
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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
• http://www.ukoln.ac.uk/projects/ebank-uk/
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The project team
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UKOLN
Michael Day
Monica Duke
Rachel Heery
Traugott Koch
Liz Lyon
+
Andy Powell
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Southampton
Les Carr
Simon Coles
Jeremy Frey
Chris Gutteridge
Mike Hursthouse
Andrew Milstead
• Manchester
• John Blunden-Ellis
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Create
Data Flow in eBank UK
HTML
Deposition
Interface
Submit
Store/link
Institutional
repository
Index
and
Search
Harvest
(XML)
eBank
aggregator
Present
HTML
Present
OAI-PMH
Deposit
Service Provider
interfaces e.g.
Subject Portal
Local archive
search
interface
JISC Joint Programmes Meeting 2005
Data files
Metadata
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Dataset
Searching,
linking and
embedding
eBank data model
Dataset
Dataset
dcterms:references
Harvesting
OAI-PMH
oai_dc
Crystal structure
(data holding)
Linking
ebank_dc
record (XML)
dc:identifier
dc:type=“CrystalStructure”
and/or “Collection”
Institutional
repository
Crystal structure
report (HTML)
Searching,
linking and
embedding
Harvesting
OAI-PMH
PSIgate
portal
ebank_dc
eBank UK
aggregator
service
dcterms:isReferencedBy
Eprint
“jump-off”
page
(HTML)
Eprint
manifestation
(e.g. PDF)
Deposit
ePrint UK
aggregator
service
dc:identifier
Linking
Model input Andy Powell, UKOLN.
Harvesting
OAI-PMH
oai_dc
Eprint oai_dc
record (XML)
dc:type=“Eprint”
and/or ”Text”
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Subject service
Searching,
linking and
embedding
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CombeChem: An EPSRC pilot project
Simulation
Video
Diffractometer
Properties
Analysis
Structures
Database
Properties
e-Lab
X-Ray
e-Lab
Grid Middleware
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Crystallography data: The publication problem
2,000,000
Cl
Cl
N
Cl
O
O
Cl
+
N O
OCl
Cl
O
Cl
Cl
Cl
O
O
+
N O
Cl
O
Cl
Cl
N
Cl
N
O
N
25,000,000
300,000
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Crystallography workflow
RAW 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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A data repository entry
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Access to the underlying data
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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Current Developments: Deposition
and validation tools
Validation
File format
manipulation
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Current Developments: Integration into
crystallographic publishing practices
Publishers seal
of approval
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Current Developments: Ontologies for
aggregating, linking & discovery
• 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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eBank : linking to learning
• Embedding in e-Learning
processes
• Evaluating the pedagogical
benefits
– MChem course
– Chemical informatics
course
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Issues and challenges
1. Issues: research data as content
• Sharing it!
• Data diversity
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Homo- or heterogeneous
Raw and derived / processed
Sensitivity
Fast or slow growth in volume
• Repository evolution:
– Likelihood to scale up (from bytes to petabytes)
– Quality assurance (from the start)
– Community-based standards development
(“folksonomies”)
– Build robust services
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2. Issues: generic data models,
metadata schema & terminology
• Validation against other schema
– CCLRC Scientific Data Model Vs 2
• Complex digital objects and packaging options
– METS
– MPEG 21 DIDL
• Terminologies
– Domain: crystallography
– Inter-disciplinary e.g. biomaterials
– Metadata enhancement: subject keyword additions to
datasets based on knowledge of keywords in related
publications
– Meaningful resource discovery?
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3. Issues: linking and identifiers
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Links to individual datasets within an experiment
Links to all datasets associated with an experiment
or a data collection
Links to derived eprints and published literature
Context sensitive linking: find me
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Datasets by this author / creator
Datasets related to this subject
Learning objects by this author / creator
Learning objects related to this subject
Identifiers and persistence
– “generic”
– domain: International Chemical Identifier (InChI code)
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Resource discovery : Google Scholar?
Provenance: authenticity, authority, integrity?
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4. Issues: embedding and workflow
• Into the crystallographic publishing community
International Union of Crystallography
• Into the chemistry research workflow
– SMART TEA Digital Lab Book e-synthesis Lab
– Other analytical techniques and instrumentation
– RAE procedures?
• Into the curriculum and e-Learning workflows
– MChem course
– Undergraduate Chemical Informatics courses
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Next in Phase 2…….
• Full embedding into the crystallographic
research and publishing communities
• Chemistry workflow embedding
– R4L Repository for the Laboratory
– Related sub-domains of chemistry SPECTRa
• e-Learning embedding and pedagogic
evaluation
– Assess role in u/g chemical informatics courses
– Introducing school children to e-research
• Enabling interdisciplinary research
– Physical, mathematical, earth, environmental and
engineering sciences
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Thank you.
Questions?…..