Transcript UK PubMed Central within the open access movement Richard Boulderstone Director of e-Strategy and Programmes British Library BioMed Central Colloquium Thursday 8th February 2007, The Royal.

UK PubMed Central within the
open access movement
Richard Boulderstone
Director of e-Strategy and Programmes
British Library
BioMed Central Colloquium
Thursday 8th February 2007, The Royal College of Physicians, London, UK
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UKPMC
‘We exist for everyone who wants to
do research – for academic, personal,
or commercial purposes.’
- BL Strategy 2005/8
‘This is the life blood of research and innovation’
Science and Innovation Investment Framework 2004-2014, H.M. Treasury (2004)
Information infrastructure
2.23 The growing UK research base must have ready and efficient access to information of all kinds – such as experimental
data sets, journals, theses, conference proceedings and patents. This is the life blood of research and innovation.
The largest document supply service
in the world. Secure e-delivery and
‘just in time’ digitisation enables
desktop delivery within 2 hours.
1.4m articles delivered in 2005/6 (80%
STM)
National library of the UK.
Serves researchers, business, libraries,
education & the general public
Over 250 years of collecting. Beneficiary
of legal deposit, and £15m annual
acquisitions budget
Generates value to the UK economy
each year of 4.4 times public funding
Collection includes over 2m sound
recordings, 5m reports, theses and
conference papers, the world’s largest
patents collection (c.50m)
Collection fills over 600km of shelving
and grows at 11km per year
1.25 Tb of digital material through
voluntary deposit
3 main funding streams:
•DCMS grant-in-aid (£89m)
•Annual trading income (£25m)
•Donations (£4m)
Helping people advance
knowledge to enrich lives
3 main sites in London and
Yorkshire. 2,250 staff
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UKPMC Project
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Based on PubMed Central (PMC) – the US National Institute of
Health (NIH) free digital archive of biomedical and life sciences
journal literature
Provides a stable, permanent and free-to-access online digital
archive of full-text, peer-reviewed research publications.
Driven by deposit mandates and recommendations from the
funders
Launched in January 2007
 Mirroring the PMC database
 Implementing a manuscript submission system - UKMSS - to
enable UK scientists to submit their research papers for
inclusion in UKPMC.
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UKPMC – The Partnership
Text
Mining and
Data
Linking
Biomedical and
Bioinformatics
Research
University of Manchester
• Hosts the service
• Builds ‘small-scale’ developments
• Engages the HE community
• Shapes future R&D
Core
Biology
Data
European Bioinformatics Institute
• Creates the links to the data
• Integrates it with other repositories
• Develops the discovery interface
Information
Services
Document
Storage and
Access
Resource
Discovery
Document
Management and
Publishing
The British Library
• Takes prime contractor role
• Manages the grantee database
• Marks up author submissions
• Creates the marketing collateral
• Promotes to the broader user community
• Provides long-term preservation
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UKPMC - Building on the Team’s experience & expertise
UKPMC is a natural fit with current business of the team members
The British Library
 Builds on existing information services and relationships with the scientific
community including NLM (2,000,000 STM Articles Delivered In 2005).
 Benefits from 10 years of expertise in the ingest, storage and preservation
of e-journals
The University of Manchester
 Gains from the University’s reputation as the major academic centre for
bioinformatics (5 & 5* Ratings in RAE 2001)
 Capitalises on MIMAS’ role as a national data centre hosting and
supporting a complex blend of services for the scientific community (e.g.
CrossFire and ISI Web of Knowledge)
The European Bioinformatics Institute
 Builds on the informatics services provided to the biomedical community
over the past 20 years including the biology datasets hosted at EBI
 Exploits existing literature-data links and services based on text mining
technologies and the close relationship with NCBI
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UKPMC build
Phase 3
Phase 2
Preservation
Full text
searching
QA
Ingest
Small-scale
developments
Phase 1
January 2007
Implement
mirror
2007-2008
2008-2010
Grant
reporting tool
Marketing
I
Integration
with
repositories
Enhanced linking
(EBI + other
datasets)
Grant
reporting tool
II
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Current Status
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Manchester
 Purchased IT infrastructure to support UKPMC, includes:
 Repository for NLM DTD formatted papers (800,000 – 2 TBytes)
 Submission system (NIHMS)
 Testing functionality in ‘standalone’ IT environment (outside NCBI)
 British Library
 Hired Marketing professional and creating marketing plan
 Selected 3rd party vendor for NLM DTD mark up and created QA
process
 Built grants database from funding organisations
 Set up help desk for authors
 EBI
 Defining strategy for future development of UKPMC
Initial Go Live = 8 January 2007
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Early Use of UKPMC
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UKPMC – embedding in the European bioscience
environment
Discovery interfaces
(e.g. Intute)
Local
‘MEDLINE plus’
Integrated with
community
interfaces
Accessed via
bibliographic
data
e-science
workbenches
Advanced
text/data mining &
visualisation
ETOC
UKPMC
Social publishing
forums & new
metrics for
authors/funders
Enhanced
content
Data supporting
interdisciplinary
research
BL
catalogue
Publisher
sites
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The Vision
Placing UKPMC at the centre of UK bioscience research
 Creating a ‘European PubMed’ – an entry point to data and
text tailored to the European domain
 Expanding the content available by providing links to the
British Library’s extensive back-catalogue and negotiating
UKPMC deposition with publishers
 Supplementing the EBI datasets by linking to the UKPMC
research archive
 Linking documents to scientific data to support the
interdisciplinary nature of research
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The Vision
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Embedding the service within the research environment – eFramework, e-science and Intute
Extending knowledge through the mining and visualising of
data, using tools being developed at EBI and Manchester
Providing new metrics for authors and funders to help
assess the quality of research
Supporting ‘social publishing’, novel peer-review
mechanisms and innovative publication discussion forums
Ensuring the permanence of UKPMC by preserving its
content in the British Library’s Digital Object Management
preservation store
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Summary
Placing UKPMC at the centre of bioscience research
 Builds on the existing strengths and synergy of the partners
 Community
 Delivery
 Preservation
 Provides a platform for the development of new services to
the UK and European biomedical research communities
 Gives us an opportunity to explore new avenues of scholarly
communication and ways of managing the outputs of
research
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