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RCUK, Octiber 2004 1
Archiving research data and research publications.
Dr Leslie Carr, Intelligence, Agents Multimedia, University of Southampton
Dr Simon Coles, School of Chemistry, University of Southampton
Dr Liz Lyon, UKOLN, University of Bath
RCUK, Octiber 2004 2
Overview
• In an Open Access environment– scientific outputs are openly available– described by appropriate metadata– in Institutional Repositories– harvestable by OAI protocols
• Scientists can use the same infrastructure– (here eprints.org software and an existing scientific portal
service)– to provide maximal open access– to all their data, as well as their published articles
• raw data, intermediate calculations, final results• in a searchable, accessible form
• BUT this is subject to ongoing investigation.
RCUK, Octiber 2004 3
Current chemistry publishing protocolsIdeas and interpretations
Results & derived data
Hooks into the literature
Raw data!
RCUK, Octiber 2004 4
Learning & Teaching workflows
Research & e-Science workflows
Aggregator services: national, commercial
Repositories : institutional, e-prints, subject, data, learning objects
Data curation: databases & databanks
Institutional presentation services: portals, Learning Management Systems, u/g, p/g courses, modules
Validation
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
Resource discovery, linking, embedding
Deposit / self-archiving
Learning object creation, re-use
Searching , harvesting, embedding
Quality assurance bodies
Validation
Presentation services: subject, media-specific, data, commercial portals
Resource discovery, linking, embedding
Linking
RCUK, Octiber 2004 5
Data Overload!
How do we disseminate?
EPSRC National Crystallography
Service
The data deluge
RCUK, Octiber 2004 6
CombeChem: An EPSRC pilot project
X-Raye-Lab
Analysis
Properties
Propertiese-Lab
SimulationVideo
Diff
ract
omet
er
Grid Middleware
StructuresDatabase
RCUK, Octiber 2004 7
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
RCUK, Octiber 2004 8
Deposition into the archive
RCUK, Octiber 2004 9
An Archive entry
ecrystals.chem.soton.ac.uk
RCUK, Octiber 2004 10
All the way back to the underlying data…
RCUK, Octiber 2004 11
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
Searching, linking and embedding
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
RCUK, Octiber 2004 12
Harvesting: OAIster
RCUK, Octiber 2004 13
Linking and aggregating: Search & discover
RCUK, Octiber 2004 14
Linking and aggregating: Hit browsing
RCUK, Octiber 2004 15
And finally…eBank embedded in a science portal