Federation

The eCrystals FederationDr Simon Coles, University of Southampton, UK

Dr Liz Lyon, UKOLN, University of Bath, UK

Open Repositories 2008, University of Southampton, April 2008

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Themes1. Context: Open science, institutional data

repositories crystallography exemplar2. Scale: repository federations3. Integration: Lab workflow and semantic

challenges 4. Longevity: Digital curation, preservation and

sustainability5. Community: DCC Data Forum

Open Science

….is happening now

• Blogging of results data

• Open grant proposals

• Community repositories for data

• Open Notebook Science (ONS) tutorials in Second Life

eBank Project – building the eCrystals Data Repository

ePrints platform @ Southampton

Institutional Repository exemplar

Embedded in workflow

http://ecrystals.chem.soton.ac.uk

Started Sept 2003

Scholarly knowledge cycle context

UKOLN-led interdisciplinary team

Scaling Up ReportInterviews & analysis of a discipline: crystallography

Synthesis: IR Policy & Practice, Laboratory Practice & Workflows, Technical Interoperability & Standards, Metadata Schema & Application Profiles, Semantic Interoperability, Data Citation, Identifiers & Linking, Federation Architectures & Third Party Services, Rights & Licensing, Data Quality & Validation, Preservation, Curation & Sustainability

Recommendations, commentary

Scaling Up Report

Phase 3 findings:

Diverse lab practice

LIMS and proprietary formats

Data policy should reflect lab practice & institutional model

Data quality criteria/validation

“Prior publication” problem

We need scalable assignment of “terms” for data discovery

No discipline preservation model

nλ = 2 d sinθ

TheThe

eCrystals Repository

ePrints.org v3.0

Repository Foundations • Using simple Dublin Core

• Crystal structure• Title (Systematic IUPAC Name)• Authors• Affiliation• Creation Date

• Additional chemical information through Qualified Dublin Core• Empirical formula• International Chemical Identifier (InChI)• Compound Class & Keywords

• Specifies which ‘datasets’ are present in an entry

• Application Profile http://www.ukoln.ac.uk/projects/ebank-uk/schemas/

• DOI links http://dx.doi.org/10.1594/ecrystals.chem.soton.ac.uk/145

• Rights & Citation http://ecrystals.chem.soton.ac.uk/rights.html

Learned society + subject repository support

Federation interoperability & linking services

• Roll-out in 2 phases led by University of Southampton• Establish Federation policies, application profile, mappings• Bi-directional links with derived articles in “publisher

repositories”, IUCr, Royal Society of Chemistry (RSC), Chemistry Central: scholarly knowledge cycle

• StOReLink project - Test linking options: StORe middleware and CLADDIER

• OAI-ORE Testbed

eChemistry project

Validation and ReproducibilityWe need to: • Provide accurate data and information that will allow an experiment to be reproduced • Record the provenance of a dataset • Provide an ‘audit trail’ from workflow capture• Relate components of a dataset to steps in the workflow• Share the workflow and record of an experiment• Provide automated approaches to validation

Laboratory practice & workflow• Community standard CIF• Mixed lab practice – central service facility

versus single “staff crystallographer” in department

• Achieve end-to-end workflow• Lack of integration with LIMS• Instrument manufacturers with proprietary

formats• “Repository Lite” for smaller lab

operations?

X-ray diffractometers

Crystallographic schema underpins CIF (Crystallographic Information Framework), but is limited to data parameters e.g. cell_length_a

Semantic issues

IUCr Acta Cryst 1992

Limited set of keywords describing methods, properties & applications, compounds, attributes

No established crystallography dictionary or controlled vocabulary to give chemistry context

Federation=Repository 2.0?• Facilitate interaction and participation beyond conventional

disciplinary boundaries• Multi-disciplinary search and browse functionality • Support tags, terms, comments, ratings…..• Automatic tag / term validation & enhancement• Develop domain semantics / vocabulary• Use domain-specific authority files • Facilitate and improve automated indexing• Link data to all associated digital objects / people• Apply across a heterogeneous Federation• Mine to “discover and innovate” rather than (just) “find”

Challenges?• How are tags, terms, comments, ratings assigned?• Informal tags and/or structured KOS? • How is a vocabulary curated and maintained?• Can a vocabulary be transformed into a (Semantic Web

related understanding) ontology?• Disambiguation, acronyms, IUPAC names• Persistent identification for data citation• Granularity of data citation: dataset or value?• Advocacy: becoming part of the lab culture

eCrystals Curation & Preservation Study

Working with the Digital Curation CentreExamined four main areas

1. Audit and certification (TRAC, DRAMBORA, NESTOR, ISO International repository audit and certification BOF Group)

2. The Open Archival Information System (OAIS) and Representation Information (RI)

3. eBank-UK application profile and preservation metadata

4. ePrints.org repository platform

Recommendations

http://www.ukoln.ac.uk/projects/ebank-uk/curation/eBank3-WP4-Report%20(Revised).pdf

eCrystals Federation: Preservation & sustainability Recommendations

Data repositories• Use DRAMBORA Interactive for self-assessment• Add PREMIS preservation metadata• Collect eCrystals representation information• Examine repository platform conformance to OAIS Reference Model• Survey partner preservation policies

Digital Curation Centre partnership

Dealing with Data Report

• DataSets Mapping and Gap Analysis (UK)

• Data Curation & Preservation Strategy (UK)

• Data Audit Framework (HE Institutions)

• Institutional Data Management, Preservation & Sharing Policy

• Data Management & Sharing Policy (Funders)

• Data Management Plan (Projects)

• Rec 5 : Data Networking Forum (People) linked to RIN Framework Principle 1

Inaugural Research Data Forum• 19-20th March 2008 in Manchester• Joint DCC – RIN event• Data centre managers, IR managers, funders & policy

makers• Aims & Objectives:

– Improve data acquisition, management, analysis, validation, archiving and dissemination

– Increase awareness of national & international data policies and standards

– Facilitate co-operation between organisations and individuals– Exchange experience and best practice

• Next meeting in autumn tbc

Heard at the Forum….“protected by PDF”

“Rembrandt in the attic”“Don’t forget the researcher!”

“stuff isn’t getting done”“demand outstrips supply…”“careers developed more by luck than judgement”“Data managers as failed scientists”

“need to sit down and write the manual”“teeth and sticks and carrots”“professionalising data management”

“Data is not just about eScience/eResearch”“we need services not projects!”

Heard at the Forum….“protected by PDF”

“Rembrandt in the attic”“Don’t forget the researcher!”

“stuff isn’t getting done”“demand outstrips supply…”“careers developed more by luck than judgement”“Data managers as failed scientists”

“need to sit down and write the manual”“teeth and sticks and carrots”“professionalising data management”

“Data is not just about eScience/eResearch”“we need services not projects!”

OR2008???OR2008???

Federation

Questions?

Slides will be available at :

http://wiki.ecrystals.chem.soton.ac.uk/index.php

http://www.ukoln.ac.uk/ukoln/staff/e.j.lyon/presentations.html

This work is licensed under a Creative Commons LicenceAttribution-ShareAlike 3.0

http://creativecommons.org/licenses/by-sa/3.0/