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

                                                             

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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.

                                                             

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Current chemistry publishing protocolsIdeas and interpretations

Results & derived data

Hooks into the literature

Raw data!

                                                             

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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

                                                             

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Data Overload!

How do we disseminate?

EPSRC National Crystallography

Service

The data deluge

                                                             

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CombeChem: An EPSRC pilot project

X-Raye-Lab

Analysis

Properties

Propertiese-Lab

SimulationVideo

Diff

ract

omet

er

Grid Middleware

StructuresDatabase

                                                             

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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

RAW DATA DERIVED DATA RESULTS DATA

                                                             

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Deposition into the archive

                                                             

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An Archive entry

ecrystals.chem.soton.ac.uk

                                                             

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All the way back to the underlying data…

                                                             

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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

                                                             

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Harvesting: OAIster

                                                             

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Linking and aggregating: Search & discover

                                                             

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Linking and aggregating: Hit browsing

                                                             

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And finally…eBank embedded in a science portal