eBank UK linking research data, scholarly communications and learning

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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
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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

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Scholarly communications
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Current chemistry publishing protocols
Ideas and interpretations
Hooks into the literature
Raw data!
Results derived data
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The government line
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.
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The scholarly knowledge cycle. Liz Lyon, eBankUK
article. Ariadne, July 2003.
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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
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The Data Publication Bottleneck
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The data deluge
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CombeChem An EPSRC pilot project
Simulation
Video
Properties
Analysis
StructuresDatabase
Diffractometer
Propertiese-Lab
X-Raye-Lab
Grid Middleware
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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
• 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
• 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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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
• Developing search interface Version 1.0
• Testing with PSIgate physical sciences portal
  embedding eBank UK

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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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Deposition into the archive
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An Archive entry
For a demo come to the JISC booth! Today _at_ 1300
during tea
ecrystals.chem.soton.ac.uk
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All the way back to the underlying data
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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
• Engaging the broader scientific community to
  ensure different schemas are compliant and
  standards can 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 jump-off page (HTML)
dcidentifier
Eprint manifestation (e.g. PDF)
Eprint oai_dc record (XML)
dctypeEprint and/or Text
Linking
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 jump-off page (HTML)
dcidentifier
Eprint manifestation (e.g. PDF)
Eprint oai_dc record (XML)
Subject service
dctypeEprint and/or Text
Linking
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 jump-off page (HTML)
dcidentifier
Eprint manifestation (e.g. PDF)
Eprint oai_dc record (XML)
Subject service
dctypeEprint and/or Text
Linking
Searching, linking and embedding
Model input Andy Powell, UKOLN.
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Harvesting OAIster
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Linking and aggregating Search discover
For a demo come to the JISC booth! Today _at_ 1300
during tea or the buffet
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Linking and aggregating Hit browsing
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And finallyeBank embedded in a science portal
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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

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Challenges for the future
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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

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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

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Thank you.Questions?..