JISC Joint Programmes Meeting 20051 eBank UK : linking research data, learning and scholarly communications. Dr Liz Lyon, UKOLN, University of Bath Dr

JISC Joint Programmes Meeting 2005 1

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

The wider context


Why create the e-Framework?The JISC strategic context

Sarah Porter, 2005

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

http://creativecommons.org/licenses/by-sa/2.0/


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



Learning object creation, re-use

Searching , harvesting, embedding

Quality assurance bodies

Validation

Presentation services: subject, media-specific, data, commercial portals


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


Data Overload!

How do we disseminate?

EPSRC National Crystallography

Service

eScience - the data deluge



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



Peer-reviewed publications: journals, conference proceedings

Publication

Validation

Data analysis, transformation, mining, modelling



Learning object creation, re-use

Searching , harvesting, embedding

Quality assurance bodies

Validation

Presentation services: subject, media-specific, data, commercial portals


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’

– 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• Traugott Koch • Liz Lyon• +• Andy Powell

• Southampton• Les Carr• Simon Coles• Jeremy Frey• Chris Gutteridge• Mike Hursthouse• Andrew Milstead

• Manchester• John Blunden-Ellis


Data Flow in eBank UK

Submit

Store/link

Data files

Metadata

Present

HTML

Institutional repository

OA

I-P

MH

Harvest (XML)

Index and Search

Present

HTML

eBank aggregator

Create

Deposition Interface

Local archive search

interface

Service Provider interfaces e.g. Subject PortalDeposit


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”

eBank data model

Eprint “jump-off” page (HTML)

dc:identifierEprint manifestation (e.g. PDF)

Linking


CombeChem: An EPSRC pilot project

X-Raye-Lab

Analysis

Properties

Propertiese-Lab

SimulationVideo

Diff

ract

omet

er

Grid Middleware

StructuresDatabase


Crystallography data: The publication problem

Cl

Cl

Cl

Cl

Cl

Cl

ClCl Cl

Cl

Cl

ClCl

O

O

O

O

N

N

N

N

N+

O

O

O

N+

O

O

O

25,000,000

2,000,000

300,000


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


A data repository entry


Access to the underlying data

ecrystals.chem.soton.ac.uk


Harvesting: OAIster


Aggregating: search & discover


Linking data to publications


eBank embedded in a science portal


Current Developments: Deposition and validation tools

Validation

File format manipulation


Current Developments: Integration into crystallographic publishing practices

Publishers seal of approval


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


eBank : linking to learning

• Embedding in e-Learning processes• Evaluating the pedagogical benefits

– MChem course

– Chemical informatics course

Issues and challenges


1. Issues: research data as content

• Sharing it!• Data diversity

– 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


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?


3. Issues: linking and identifiers

• 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

– 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)

• Resource discovery : Google Scholar?• Provenance: authenticity, authority, integrity?


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


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

Thank you.

Questions?…..

Documents

JISC Joint Programmes Meeting 20051 eBank UK : linking research data, learning and scholarly communications. Dr Liz Lyon, UKOLN, University of Bath Dr