The eCrystals Federation

Dr 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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Federation

Themes

1. Context: Open science, institutional data repositories crystallography exemplar 2. Scale: repository federations 3. Integration: Lab workflow and semantic challenges 4. Longevity: Digital curation, preservation and sustainability 5. 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 Started Sept 2003

Scholarly knowledge cycle context

UKOLN-led

interdisciplinary team

ePrints platform @ Southampton Institutional Repository exemplar Embedded in workflow

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

Scaling Up Report

Interviews & 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

The nλ = 2 d sinθ

eCrystals Repository ePrints.org v3.0

Repository Foundations

Learned society + subject repository support

• 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

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 Reproducibility

• We 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

Semantic issues

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

No established crystallography dictionary or controlled vocabulary to give chemistry context IUCr Acta Cryst 1992 Limited set of keywords describing methods, properties & applications, compounds, attributes

• • • • • • • • • •

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 Centre Examined four main areas 1.

Audit and certification (TRAC, DRAMBORA, NESTOR, ISO International repository audit and certification BOF Group) 2.

3.

4.

The Open Archival Information System (OAIS) and Representation Information (RI) eBank-UK application profile and preservation metadata ePrints.org repository platform

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

Recommendations

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

• • • • • 19-20 th 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

“ protected by PDF ”

Heard at the Forum….

“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!”

“ protected by PDF ”

Heard at the Forum….

“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!”

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 Licence Attribution-ShareAlike 3.0

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

Federation