Federation eCrystals Federation: Open Repositories for Open Science Dr Liz Lyon, UKOLN, University of Bath, UK Dr Simon Coles, University of Southampton,

Federation

eCrystals Federation: Open Repositories for Open Science

Dr Liz Lyon, UKOLN, University of Bath, UK

Dr Simon Coles, University of Southampton, UK

Dr Manjula Patel, UKOLN, University of Bath, UK

CNI Taskforce Meeting, Washington DC, December 2007

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1. Chemistry and Open Science : context and practice.

2. Lessons learnt from eBank Phase 3

3. Data curation and preservation issues

4. Setting up the Federation: Challenges ahead?

Overview

Federation

Chemistry and Open Science: context and practice

Social networks for chemists….

New postgraduate cohorts : millennials / Google generation : new behaviours

Community content for chemists : rich media

video + paper = Pubcast

>8000 views

At the coalface: tagging & sharing workflows Astronomy, Bioinformatics, Chemistry, Social Science pilots.

Universities of Manchester & Southampton

“Small science” : sharing in the lab

Open Wetware Laboratory wikis

Transforming practice?

2006

Open Notebook Science (ONS)

26 September:

1st use of term blogged by Jean-Claude Bradley, Drexel University

2007

27 March: ONS at

Amer Chem Society Symposium

7 August: ONS Poster in Second Life on Nature island

24 September: ONS Case Studies in Second Life

4 October: > 43,000 hits in Google for term ONS

10 & 15 October: Policy lists,DabbleDB membership database created US

11 October: ONS experiment starts in Cambridge, UK

7 November: Cameron Neylon (Univ Southampton / STFC, UK) posts “Sourceforge for Science” concept

10 November: Open Data for common molecules - Wikichemicals? Peter Murray-Rust’s blog at Univ. Cambridge, UK

27 November: Research Network proposal submitted to UK research council

Yesterday: about 2,400,000 Google hits for Open Notebook Science

New ideas are surfacing very fast with instant development, testing and take-up…..

eBank Project – building the eCrystals Data Repository

Institutional Repository exemplar

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

Metadata Publication• 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

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

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

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

blogswikis

HarvestPublish

Federation

Lessons learnt from eBank Phase 3

• Scoping the eCrystals Federation of crystallography data repositories

• Questionnaire and interview-based • Joint Consultation Workshop (eBank, R4L, SPECTRa) & Report• Engage whole data lifecycle community – crystallographers,

central facilities, publishers, data centres, and chemical information specialists.

• Mixed project team: Chemists, Digital Library researchers & Computer Scientists

Study Aims and Approach

Lessons: Policy and practice• Must be considered at level of the Institution and the

practising Laboratory• Mixed lab practice – central service facility versus single

“staff crystallographer” in department• “Repository Lite” for smaller lab operations?• Established data ‘publication’ practice + domain subject

repository: Cambridge Crystallographic Data Centre (CCDC)

• Institutional policy buy-in is essential• Demonstrate benefits and added value to senior managers• Implications for information services structure

Interoperability & Standards

• Instrument manufacturers proprietary formats

• Technical software platform• Metadata schema : Application profiles• Standards and identifiers –

International Chemical Identifier (InChI), DOI, CIF, CML, de facto software

• Semantic interoperability

X-ray diffractometers

Subject Repositories, Publishing and IPR

• Established subject repository at CCDC (40 years old!) : repository interactions?

• The “embargo problem” : prior dissemination affecting publication of journal article

• Cultural issues related to chemists “its my data” (journal article will always be sacred)

• Mechanisms for sharing with collaborators and referees prior to publication?

Advocacy

• The most important issue?!?

Federation

Data curation and preservation issues

Digital Curation Centre http://www.dcc.ac.uk/

• Community Development work

• Led by UKOLN • eBank/eCrystals

partner

eBank-UK Phase 3 Curation & Preservation Study

http://www.ukoln.ac.uk/projects/ebank-uk/curation/

Examined four main areas1. 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

Observations & Recommendations 1• Self-assessment using DRAMBORA toolkit• Engage DCC audit & certification team• Formulation of long-term objectives and policy

– Deposit agreements– Services

• Aim for community-supported sustainability plan• Implement regular audits: annual• Produce evidence of compliance

– Documentation– Transparency– Adequacy– Measurability

• Federation context

Observations & Recommendations 2

• Maintenance and open access of critical file formats and software– Work-up software e.g. XPREP– Export raw data from instrumentation as imgCIF

• Consider Representation Information (RI) in context of whole crystallography landscape (CCDC, IUCR etc.) • Develop a preservation and curation strategy and formal policies to indicate levels of service

– Deposit, ingest, validation, dissemination

• Consider services to be developed over the DCC Registry/Repository of Representation Information (RRoRI)

Observations & Recommendations 3• Develop preservation strategy & plan for the specific content • Capture preservation metadata, including versioning and provenance information• PREMIS Data Dictionary

– Semantic Units (e.g. file format, significant properties, provenance, fixity info)

– Extend eBank metadata application profile (AP)?

• Obtain consensus on AP• Seek to automate metadata generation, extraction, maintenance• ePrints.org support for information packages

Federation

Setting up the Federation: Challenges ahead?

CreateDeposit

Link

Curate Preserve Standards

Scientist

Funder

Collaborate Share

User

Discover Re-use

eCrystals Federation Data Deposit Model

Link

Link

Scientist

Policy AdvocacyTraining

HarvestIR Federation

Publishers

Data centres / aggregator

servicesAdvisory

Repository deployment & support

• Roll-out in 2 phases– Universities Sydney, Glasgow, Newcastle with

eprints.org platform– Universities Cambridge, STFC, ReciprocalNet,

ARCHER with other platforms

• Information Environment Service Registry (IESR) listing Federation Collections

Raw Data

Public domain material

Laboratory Workflow & Provenance• Achieving end-to-end

workflows: avoiding fragmentation of data, results and interpretations

• Account for differinglaboratory practice

RAW DATA DERIVED DATA RESULTS DATA

Repository interoperability & linking services

• Establish core Federation application profile and mappings

• Bi-directional links with derived articles in “publisher repositories”, IUCr, Royal Society of Chemistry (RSC), Chemistry Central

• Test linking options: StORe middleware and CLADDIER (JISC-funded projects)

• OAI-ORE Pathways Project developments

Interoperability testbed• Experimental data sets + metadata as compound objects• Dublin Core and METS not sufficient• OAI-ORE (base: Atom Publishing Protocol) testbed• Enable 3rd party services e.g. data / text mining

eChemistry project

Enabling data discovery

• Royal Society of Chemistry Project Prospect tagging & semantic linking

Preservation & Sustainability• DRAMBORA Assessment : use DRAMBORA Interactive• Enhance Application Profile with PREMIS preservation metadata• Populate RRoRI with crystallography representation information• Examine repository platform conformance to OAIS Ref Model

• Survey partner institutional preservation policies

Embedding into current publishing practice• Chemists still want to publish scholarly articles• Blogs and repositories are a new form of rapid

communication, but there are prior publication concerns• Timing of release of data into public domain and formal

publication will be crucial – Repository must provide control over timing of public visibility – EPrints3 version of eCrystals has ‘embargo tokens’

• Validation and quality in an ‘Open’ world– Quality indicators?

Advocacy• Chemists still wary of ‘Open Access’• eCrystals Roadshow Workshops

engaging both crystallographers and their service ‘users’ in the workplace

• Open forum at International Union of Crystallography world congress (Aug 2008)

• Publishers Workshop to demonstrate co-existence of open data models & traditional scholarly articles

Federation

Questions?

Slides will be available at :

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

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