eBank UK - linking research data, scholarly communications and learning

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eBank UK linking research data, scholarly
communications and learning. Dr Liz Lyon,
UKOLN, University of Bath, UK JISC CNI
Conference July 2004, Brighton.
UKOLN is supported by
www.bath.ac.uk
www.ukoln.ac.uk
a centre of expertise in digital information
management
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Overview

• Setting the scene e-Research
• The scholarly knowledge cycle
• Data, information and workflows
• Provenance
• eBank UK Project
• The experience so far
• Issues arising
• Challenges for the future

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Setting the scene e-Research
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e-Research trends summary

• Increasingly dataintensive, quantitative
• Implementing new science
• Inter-disciplinary
• New disciplines e.g. Astro-informatics
• New skills requirements
• IT statistics domain
• Collaborative
• Highly distributed resources
• Knowledge discovery / extraction
• Open access to data and information
• OECD Declaration January 2004
• A changing landscape of scholarly communications

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The scholarly knowledge cycle
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Presentation services subject, media-specific,
data, commercial portals
Searching , harvesting, embedding
Resource discovery, linking, embedding
Data creation / capture / gathering laboratory
experiments, Grids, fieldwork, surveys, media
The scholarly knowledge cycle. Liz Lyon, eBankUK
article. Ariadne, July 2003.
Aggregator services national, commercial
Data analysis, transformation, mining, modelling
Harvestingmetadata
Research e-Science workflows
Repositories institutional,
e-prints, subject, data, learning objects
Deposit / self-archiving
Validation
Validation
Publication
Linking
Peer-reviewed publications journals, conference
proceedings
Data curation databases databanks
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Presentation services subject, media-specific,
data, commercial portals
Searching , harvesting, embedding
Resource discovery, linking, embedding
Data creation / capture / gathering laboratory
experiments, Grids, fieldwork, surveys, media
Aggregator services national, commercial
Data analysis, transformation, mining, modelling
Harvestingmetadata
Research e-Science workflows
Repositories institutional,
e-prints, subject, data, learning objects
Deposit / self-archiving
Validation
Validation
Publication
Linking
Peer-reviewed publications journals, conference
proceedings
Data curation databases databanks
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Presentation services subject, media-specific,
data, commercial portals
Searching , harvesting, embedding
Resource discovery, linking, embedding
Data creation / capture / gathering laboratory
experiments, Grids, fieldwork, surveys, media
Aggregator services national, commercial
Data analysis, transformation, mining, modelling
Harvestingmetadata
Research e-Science workflows
Repositories institutional,
e-prints, subject, data, learning objects
Deposit / self-archiving
Validation
Validation
Publication
Linking
Peer-reviewed publications journals, conference
proceedings
Data curation databases databanks
15
Presentation services subject, media-specific,
data, commercial portals
Searching , harvesting, embedding
Resource discovery, linking, embedding
Aggregator services national, commercial
Learning object creation, re-use
Harvestingmetadata
Learning Teaching workflows
Repositories institutional,
e-prints, subject, data, learning objects
Institutional presentation services portals,
Learning Management Systems, u/g, p/g courses,
modules
Deposit / self-archiving
Validation
Resource discovery, linking, embedding
Validation
Peer-reviewed publications journals, conference
proceedings
Quality assurance bodies
16
Presentation services subject, media-specific,
data, commercial portals
Searching , harvesting, embedding
Resource discovery, linking, embedding
Resource discovery, linking, embedding
Data creation / capture / gathering laboratory
experiments, Grids, fieldwork, surveys, media
Aggregator services national, commercial
Data analysis, transformation, mining, modelling
Learning object creation, re-use
Harvestingmetadata
Learning Teaching workflows
Research e-Science workflows
Repositories institutional,
e-prints, subject, data, learning objects
Institutional presentation services portals,
Learning Management Systems, u/g, p/g courses,
modules
Deposit / self-archiving
Deposit / self-archiving
Validation
Validation
Publication
Resource discovery, linking, embedding
Validation
Linking
Peer-reviewed publications journals, conference
proceedings
Quality assurance bodies
Data curation databases databanks
17
Presentation services subject, media-specific,
data, commercial portals
Searching , harvesting, embedding
Resource discovery, linking, embedding
Resource discovery, linking, embedding
Data creation / capture / gathering laboratory
experiments, Grids, fieldwork, surveys, media
Data analysis, transformation, mining, modelling
Learning object creation, re-use
Aggregator services eBank UK
Harvestingmetadata
Learning Teaching workflows
Research e-Science workflows
Repositories institutional,
e-prints, subject, data, learning objects
Institutional presentation services portals,
Learning Management Systems, u/g, p/g courses,
modules
Deposit / self-archiving
Deposit / self-archiving
Validation
Validation
Publication
Resource discovery, linking, embedding
Validation
Linking
Peer-reviewed publications journals, conference
proceedings
Quality assurance bodies
Data curation databases databanks
18
The eBank UK Project
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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
• e-Science testbed Combechem
• Grid-enabled combinatorial chemistry
• Crystallography, laser and surface chemistry
• 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

• 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

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Comb-e-Chem Project
Video
Simulation
Properties
Analysis
StructuresDatabase
Diffractometer
X-Raye-Lab
Propertiese-Lab
Grid Middleware
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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

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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

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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
• Develop search interface Version 1.0
• Testing with PSIgate physical sciences portal
  embedding eBank UK

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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
• Will substitute when standards emerge

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Dataset
Data flow in eBank
Dataset
Dataset
dctermsreferences
Crystal structure (data holding)
Linking
ebank_dc record (XML)
Deposit
dctypeCrystalStructure and/or Collection
Institutional repository
dcidentifier
Crystal structure report (HTML)
dctermsisReferencedBy
Eprint oai_dc record (XML)
dctypeEprint and/or Text
Model input Andy Powell, UKOLN.
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Dataset
Data flow in eBank
Dataset
Dataset
dctermsreferences
Harvesting OAI-PMH oai_dc
Crystal structure (data holding)
ePrint UK aggregator service
Linking
Harvesting OAI-PMH ebank_dc
ebank_dc record (XML)
Deposit
dctypeCrystalStructure and/or Collection
eBank UK aggregator service
Institutional repository
dcidentifier
Crystal structure report (HTML)
dctermsisReferencedBy
Harvesting OAI-PMH oai_dc
Eprint oai_dc record (XML)
dctypeEprint and/or Text
Subject service
Model input Andy Powell, UKOLN.
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Searching, linking and embedding
Dataset
Data flow in eBank
Dataset
Dataset
dctermsreferences
Harvesting OAI-PMH oai_dc
Crystal structure (data holding)
ePrint UK aggregator service
Linking
Searching, linking and embedding
Harvesting OAI-PMH ebank_dc
ebank_dc record (XML)
Deposit
PSIgate portal
dctypeCrystalStructure and/or Collection
eBank UK aggregator service
Institutional repository
dcidentifier
Crystal structure report (HTML)
dctermsisReferencedBy
Harvesting OAI-PMH oai_dc
Eprint oai_dc record (XML)
dctypeEprint and/or Text
Subject service
Searching, linking and embedding
Model input Andy Powell, UKOLN.
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Currently we are

• Planning Consultation Workshop August
• Developing a demonstrator
• Promoting Open Access and Open eData Archives to
  international crystallographic organisations,
  publishers, learned societies
• e-Science All Hands Meeting, Nottingham September
  2004.
• Phase 2 proposal funding sought for further 12
  months

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Challenges for the future
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Phase 2 plan.(1)

• Continue to progress generic data models and
  metadata schemas
• Validation against other schema
• CLRC Scientific Metadata Model vs 1.0 2001 (under
  revision)
  http//www-dienst.rl.ac.uk/library/2002/tr/dltr-20
  02001.pdf
• Complex digital objects
• Investigate packaging options
• METS
• MPEG 21 DIDL
• ??
• Metadata enhancement - subject keyword additions
  to datasets based on knowledge of keywords in
  related publications

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Phase 2..(2)

• Investigate identifiers e.g. International
  Chemical Identifier (InChI code)
• Access to scientific (climate) data using DOIs
  (German National Library of Science Technology)
  
• 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

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Phase 2.(3)

• Workflow embedding
• Expand to include SMART e-Lab metadata e.g.
  sample preparation
• e-Learning embedding and pedagogic evaluation
• MChem course
• Chemical informatics course
• Expand into other physical sciences
• Feasibility study in a related domain -
  biosciences

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Presentation services subject, media-specific,
data, commercial portals
Searching , harvesting, embedding
Resource discovery, linking, embedding
Resource discovery, linking, embedding
Data creation / capture / gathering laboratory
experiments, Grids, fieldwork, surveys, media
Data analysis, transformation, mining, modelling
Learning object creation, re-use
Aggregator services eBank UK
Harvestingmetadata
Learning Teaching workflows
Research e-Science workflows
Repositories institutional,
e-prints, subject, data, learning objects
Institutional presentation services portals,
Learning Management Systems, u/g, p/g courses,
modules
Deposit / self-archiving
Deposit / self-archiving
Validation
Validation
Publication
Resource discovery, linking, embedding
Validation
Linking
Peer-reviewed publications journals, conference
proceedings
Quality assurance bodies
Data curation databases databanks
36
Potential longer term impact

1. Track data, information and workflows in
   e-research and scholarly communications
   knowledge audit??
2. Validate the accuracy and authenticity of derived
   works ideas audit??
3. Facilitate explicit referencing and
   acknowledgment of original contributors
   intellectual integrity??
4. Raise standards associated with publication of
   research outputs academic publishing rigour??
5. Implement open access to and dissemination of
   data and information enhance the research
   process??
6. Give students links to original data underpinning
   published works enhance the learning process??

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Thank you.Questions?..