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

AHM, Nottingham, September 2004 1

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


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

Scholarly communications


Current chemistry publishing protocols

Ideas and interpretations

Results & derived data

Hooks into the literature

Raw data!




“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


Research & e-Science workflows

Aggregator services: national, commercial

Repositories : institutional, e-prints, subject, data, learning objects

Data curation: databases & databanks

Validation

Harvestingmetadata

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.


Learning & Teaching workflows



Institutional presentation services: portals, Learning Management Systems, u/g, p/g courses, modules

Harvestingmetadata



Validation



Learning object creation, re-use


Quality assurance bodies

Validation









Validation

Harvestingmetadata





Publication

Validation







Validation



Linking




Aggregator services:

eBank UK




Validation

Harvestingmetadata





Publication

Validation







Validation



Linking

The Data Publication Bottleneck


Data Overload!

How do we disseminate?

EPSRC National Crystallography

Service

The data deluge


CombeChem: An EPSRC pilot project

X-Raye-Lab

Analysis

Properties

Propertiese-Lab

SimulationVideo

Diff

ract

omet

er

Grid Middleware

StructuresDatabase


Grid

E-Scientists

Entire E-Science CycleEncompassing experimentation, analysis, publication, research, learning

5

Institutional Archive

LocalWebPublisher

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

The eBank UK Project


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/


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


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


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


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 DATA DERIVED DATA RESULTS DATA


Deposition into the archive


An Archive entry

ecrystals.chem.soton.ac.uk

For a demo come to the JISC booth!

Today @ 13:00 & during tea


All the way back to the underlying data…


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


ebank_dc record (XML)

Crystal structure (data holding)

Crystal structure report (HTML)

Dataset

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:identifierEprint manifestation (e.g. PDF)

Linking


ebank_dc record (XML)

Crystal structure (data holding)

Crystal structure report (HTML)

Dataset

Dataset

Institutional repository

eBank UK aggregator service

ePrint UK aggregator service

Subject service

DepositHarvesting OAI-PMH

ebank_dc

Harvesting OAI-PMH oai_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:identifierEprint manifestation (e.g. PDF)

Linking


Harvesting: OAIster


Linking and aggregating: Search & discover

For a demo come to the JISC booth!Today @ 13:00 & during tea or the buffet


Linking and aggregating: Hit browsing


And finally…eBank embedded in a science portal


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

Challenges for the future


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


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

Thank you.

Questions?…..

Documents

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