Biomedical resource site contract awarded to University and partners
28 Jul 2011
The University of Manchester, in partnership with the British Library and the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI), has been awarded the contract to run and develop UK PubMed Central (UKPMC), the free online literature resource for life science researchers.
Now five years old, UKPMC has grown from a simple mirror of the National Center for Biotechnology Information (NCBI) PubMed Central site to a stand-alone site providing access to a repository of more than 2 million full-text biomedical research articles, more than 25 million citations from PubMed and Agricola, patents from the European Patent Office, UK treatment guidelines and biomedical PhD theses.
Content is discoverable through an integrated full-text and abstract search and is semantically enriched by the application of cutting-edge text-mining approaches. Over 250,000 articles in this valuable resource are published under open-access licenses, which means their contents can be freely reused.
The UK funding organisations that support UKPMC want to build upon this success through a new five-year contract awarded to the partnership. The goal is to build a gold-standard digital repository for the biomedical literature that benefits life science researchers throughout the world.
EMBL-EBI, as lead partner, will contribute its biomedical domain knowledge and text-mining tools to continue to integrate the research literature with the underlying bioinformatics databases. EMBL-EBI will now run the main service, while the British Library will lead promotion to researchers, as well as offering support for researchers depositing their papers in UKPMC.
The University of Manchester’s Faculty of Life Sciences supports the process of engaging with higher education users through its bioinformatics expertise, while Mimas, the JISC & Research Council-funded national academic data centre based at the University, manages and runs the core technical components of the manuscript submission service and develops and hosts the grant reporting service. The National Centre for Text Mining (NaCTeM), based in the School of Computer Science within the University’s Manchester Interdisciplinary Biocentre, leads the development of advanced text-mining techniques to extract evidence from text, such as genes, proteins, chemicals, diseases, etc, and their relations – a sort of ‘Ask Jeeves’ for bioscientists.
Professor Simon Hubbard, who leads the overall Manchester-based effort, as well as acting as a consultant on user engagement, said: “The next phase of UKPMC promises to see real advances for biomedical scientists, supporting new ways to search the literature for undiscovered information, with even more links out to data and additional content.”
The service will be funded by a significantly expanded group of funding organisations: eight funders launched the service in 2007; the new contract sees the participation of 18 UK and European funders, led by the Wellcome Trust.
Sir Mark Walport, Director of the Wellcome Trust, said: “We are delighted that additional funders are supporting UKPMC and requiring the outputs of the research they fund to be made freely available through this open access repository. We want to build on the success of the past five years and, in partnership with research funders across Europe, transform UKPMC into a single, Europe-wide, open-access repository for the life sciences.”
Over the next five years, UKPMC funders will continue to seek the involvement of scientific publishers as well as a broad range of funding agencies, universities and other research institutions in order to better serve research communities throughout Europe and beyond.
Notes for editors
About UK PubMed Central:
UK PubMed Central (UKPMC) is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. The UKPMC project was launched in 2007 under the leadership of the British Library, as the first ‘mirror’ site to PMC, which aims to provide international preservation of the open and free-access biomedical literature. UKPMC has undergone considerable development since its inception, and now includes both a UKPMC and a PubMed search, as well as access to other records such as Agricola, Patents and recent biomedical theses. UKPMC also differs from PubMed/PMC in that the full text and abstract information can be searched in an integrated manner from one input box. Furthermore, UKPMC contains ‘Cited By’ information as an alternative way to navigate the literature and has incorporated text-mining approaches to semantically enrich content and integrate it with related database resources. Finally, UKPMC also offers added-value services (UKPMC+) that enable grantees to deposit manuscripts, link papers to grants, publish online portfolios and view citation information on their papers.
About UKPMC Funders' Group:
Led by the Wellcome Trust, the UKPMC Funders’ Group comprises the following funding organisations: Action on Hearing Loss, Arthritis Research UK, Austrian Science Fund (FWF), Biotechnology and Biosciences Research Council, Breakthrough Breast Cancer, British Heart Foundation, Cancer Research UK, The Chief Scientist Office of the Scottish Government Health Directorates, The Dunhill Medical Trust, Marie Curie Cancer Care, Medical Research Council, the Motor Neurone Disease Association, the Multiple Sclerosis Society, Parkinson’s UK, Myrovlytis Trust, National Institute for Health Research (Department of Health), Telethon (Italy).
The European Molecular Biology Laboratory is a basic research institute funded by public research monies from 20 member states (Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom) and associate member state Australia. Research at EMBL is conducted by approximately 85 independent groups covering the spectrum of molecular biology. The Laboratory has five units: the main Laboratory in Heidelberg, and Outstations in Hinxton (the European Bioinformatics Institute), Grenoble, Hamburg, and Monterotondo near Rome. The cornerstones of EMBL’s mission are: to perform basic research in molecular biology; to train scientists, students and visitors at all levels; to offer vital services to scientists in the member states; to develop new instruments and methods in the life sciences and to actively engage in technology transfer activities. Around 190 students are enrolled in EMBL’s International PhD programme. Additionally, the Laboratory offers a platform for dialogue with the general public through various science communication activities such as lecture series, visitor programmes and the dissemination of scientific achievements.
The European Bioinformatics Institute (EBI) is part of the European Molecular Biology Laboratory (EMBL) and is located on the Wellcome Trust Genome Campus in Hinxton near Cambridge (UK). The EBI grew out of EMBL's pioneering work in providing public biological databases to the research community. It hosts some of the world’s most important collections of biological data, including DNA sequences (EMBL-Bank), protein sequences (UniProt), animal genomes (Ensembl), three-dimensional structures (the Protein Databank in Europe), data from gene expression experiments (ArrayExpress), protein-protein interactions (IntAct) and pathway information (Reactome). The EBI hosts several research groups and its scientists continually develop new tools for the biocomputing community.
About the British Library:
The British Library is the national library of the United Kingdom and one of the world's greatest research libraries. It provides world class information services to the academic, business, research and scientific communities and offers unparalleled access to the world's largest and most comprehensive research collection. The Library's collection has developed over 250 years and exceeds 150 million separate items representing every age of written civilisation and includes books, journals, manuscripts, maps, stamps, music, patents, photographs, newspapers and sound recordings in all written and spoken languages. Up to 10 million people visit the British Library website - www.bl.uk - every year where they can view up to 4 million digitised collection items and over 40 million pages.
About the University of Manchester:
The University of Manchester, a member of the Russell Group, is one of the largest and most popular universities in the UK. It has 22 academic schools and hundreds of specialist research groups undertaking pioneering multi-disciplinary teaching and research of worldwide significance. According to the results of the 2008 Research Assessment Exercise, The University of Manchester is now one of the country’s major research institutions, rated third in the UK in terms of ‘research power’. The University had an annual income of £788 million in 2009/10.
For further information contact:
Faculty of Life Sciences
The University of Manchester
Tel: 0161 275 8383
Mob: 07717 881563