eCrystals Federation

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eCrystals Federation Open Repositories for
Data-driven Science Dr Liz Lyon, UKOLN,
University of Bath, UK Dr Simon Coles, University
of Southampton, UK Chemical Informatics
Workshop, Manchester, March 2008
Federation
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Themes

• Context Institutional data repositories
  crystallography exemplar
• Scale repository federations
• Longevity Digital curation and preservation
• Integration Semantic challenges

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eBank Project building the eCrystals Data
Repository
Started Sept 2003 Scholarly knowledge cycle
context UKOLN-led interdisciplinary team
ePrints platform _at_ Southampton Institutional
Repository exemplar Embedded in
workflow http//ecrystals.chem.soton.ac.uk
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Scaling Up Report Phase 3 findings Data policy
should reflect lab practice institutional
model Diverse lab practice LIMS proprietary
formats Data quality criteria/validation Prior
publication problem We need automated assignment
of terms for data discovery No discipline
preservation model
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The
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eCrystals Repository ePrints.org v3.0
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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/projec
  ts/ebank-uk/schemas/
• DOI links http//dx.doi.org/10.1594/ecrystals.che
  m.soton.ac.uk/145
• Rights Citation http//ecrystals.chem.soton.ac.
  uk/rights.html

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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
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Laboratory practice workflow

• Community standard CIF
• Mixed lab practice central service facility
  versus single staff crystallographer in
  department
• Achieve end-to-end workflow
• Challenge of instrument manufacturers with
  proprietary formats
• Repository Lite for smaller lab operations?

X-ray diffractometers
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eBank-UK Phase 3 Curation Preservation Study
Sustainability issues

• http//www.ukoln.ac.uk/projects/ebank-uk/curation/
  
• Examined four main areas
• Audit and certification (TRAC, DRAMBORA, NESTOR,
  ISO International repository audit and
  certification BOF Group)
• The Open Archival Information System (OAIS) and
  Representation Information (RI)
• eBank-UK application profile and preservation
  metadata
• ePrints.org repository platform

Recommendations Self-assessment using
DRAMBORA Consider Representation Information in
wider context Develop preservation
strategy Capture preservation metadata - PREMIS
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Semantic issues

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

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• 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

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What do we want to do?

• Support depositors keyword/term assignment
• Facilitate and improve automated indexing
• Support advanced search / browse
• Allow metadata validation enhancement
• Apply across a heterogeneous Federation
• Cross search, cross browse functionality
• Link data to all associated digital objects
• Develop domain semantics / vocabulary
• Use domain-specific authority files
• Mine to discover rather than find
• Achieve full inter-disciplinary integration

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Some (semantic) issues..

• How are terms 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
• Data (and metadata) quality, provenance,
  validation
• Embedding within complex workflows
• Use collaborative social approaches?
• Community adoption becomes part of the culture

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Questions? Slides will be available at
http//wiki.ecrystals.chem.soton.ac.uk/index.ph
p http//www.ukoln.ac.uk/ukoln/staff/e.j.lyon/pres
entations.html
Federation