Tuesday, 8 November 2011

Editorial team announced for ‘eLife’, the new open access journal to be launched next year

The senior editorial team is today announced for ‘eLife’, the new top-tier, open access research journal to be launched next year with the support of the Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust.

Read the press release on the Wellcome Trust website.

Tuesday, 25 October 2011

Two reports from the UK Open Access Implementation Group (OAIG)

Yesterday the UK OAIG released research reporting on the benefits of open access to commercial companies and findings from a JISC Collections consultation on the practicalities of paying for open access publication.

Links
Benefits to the Private Sector of Open Access to Higher Education and Scholarly Research
Open Access Fees Report

OAIG press release (24 October)

Monday, 17 October 2011

Open Biology - a new open access journal

Today is the official launch of the Royal Society's first wholly open access and online journal - Open Biology.

The new journal is publishing research in cell biology, developmental and structural biology, molecular biology, biochemistry, neuroscience, immunology, microbiology and genetics. It is overseen by a team of academic Subject Editors with support by an international Editorial Board. Professor David Glover FRS, Cambridge University has been appointed Editor-in-Chief.

Open Biology aims to have a turnaround time of 4 weeks from article submission to first decision.

Read more on the journal website.

Tuesday, 11 October 2011

Mark Patterson named Managing Executive Editor of new open access journal

Mark Patterson
Dr Mark Patterson, director of publishing at the Public Library of Science (PLoS), has been named managing executive editor of a new open-access research journal that the Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust are launching next year.
 
Further details are available at the Wellcome Trust web site.

Friday, 2 September 2011

The Open Access Interviews

In the latest of his Open Access Interviews, freelance journalist Richard Poynder interviews Robert Kiley from the Wellcome Trust about the Trust's policy with regard to paying OA publication fees.

Wednesday, 31 August 2011

UKPMC is hiring!

Project Manager for UKPMC
We are looking to recruit an experienced Project Manager to join the Literature Services Team at the European Bioinformatics Institute (EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK.

The Project Manager will be responsible for coordinating UK PubMed Central (UKPMC), a repository of 2 million full text biomedical research articles, supplemented with over 25 million abstracts, database links and citation information. UKPMC is being developed by groups at the EBI, the British Library, and the University of Manchester and is funded by all major UK funders of biological and biomedical research, led by the Wellcome Trust.

We are looking for an experienced Project Manager to run the core UKPMC project. This is an excellent opportunity to contribute to an ambitious project that aims to become the literature resource of choice for life science and biomedical researchers in the UK, Europe and beyond.

More details and a full job description are available on the EBI website.

Friday, 29 July 2011

European Bioinformatics Institute to lead UK PubMed Central

The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) has been awarded the contract to run and lead the development of 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 USA-based National Center for Biotechnology Information PubMed Central site to a stand-alone site providing access to a repository of more than two 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 via an integrated full text and abstract search and is semantically enriched by the application of cutting-edge text mining approaches. More than 250 000 articles are published under open-access licenses, which means their contents can be freely reused.

The UK funding organisations that support UKPMC wish to build upon this success through a new five-year contract awarded to EMBL-EBI, who will lead the development of the service in partnership with the University of Manchester and the British Library. The goal is to build a gold-standard digital repository for biomedical literature that benefits life science researchers throughout the world.

"We want to help researchers make the best possible use of the scientific literature by building deep content links between articles and the underlying data," said Dr Johanna McEntyre, Head of Literature Services at EMBL-EBI. "If we manage that, UKPMC will give people a chance to navigate the biomedical information space in an intuitive way."

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.

"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," said Sir Mark Walport, Director of the Wellcome Trust. "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, UK PubMed Central funders will continue to seek the involvement of scientific publishers as well as a broad range of funding agencies, universities and other research institutions to better serve research communities throughout Europe and beyond.

Read the press release at the Wellcome Trust, EMBL-EBI and the University of Manchester.

Monday, 11 July 2011

UKPMC Engagement Manager vacancy

Engagement Manager

UK PubMed Central

British Library

St Pancras, London
UK PubMed Central (UKPMC) is a unique, innovative online resource offering free access to full text journal articles, abstracts, clinical guidelines, theses and biological databases for biomedical and health researchers. As UKPMC enters an exciting new phase, we need an experienced biomedical researcher who will lead on engagement to raise awareness of UKPMC and communicate its benefits.
In this high profile role, you be responsible for the UKPMC brand through print, press and social media, complemented by an extensive programme of seminars, demonstrations, networking, and other promotional activity. Dynamic and confident, you'll have the credibility and communication skills needed to work successfully with multiple stakeholders across the biomedical and health research sector.
You will have an understanding of web-based biomedical resources, how they are utilised by researchers, as well as an interest in emerging trends in this area. You will use this knowledge, along with your experience in engagement and communication, to develop innovative ways to highlight the benefits of UKPMC to the scientific research community and beyond.
For more information and to apply, visit www.bl.uk/vacancies and search under Ref EIS00149.
Closing date: 20 July 2011.

Tuesday, 5 July 2011

UKPMC -- now with links to records held in the Centre for Reviews and Dissemination (CRD) databases

A core strategy of the development of UKPMC has been to help users access, (through a single search interface), a range of relevant information, in addition to peer-reviewed journal articles, that could prove useful in their research.  Since the launch of the new service in June 2010, we have provided links to an increasing number of PhD theses and clinical guidelines, as well as a range of research reports.

The latest enhancement is the inclusion of links to databases maintained by the Centre for Reviews and Dissemination (CRD), part of the National Institute for Health Research (NIHR).

The CRD provides research-based information about the effects of health and social care interventions via its databases and undertakes systematic reviews evaluating the research evidence on health and public health questions of national and international importance.

The CRD databases, updated daily, provide access to:

• Over 9,000 quality assessed systematic reviews

• Over 11,000 economic evaluations

• Over 10,000 summaries of completed and ongoing health technology assessments

• Summaries of all Cochrane reviews and protocols

• Summaries of Campbell reviews

Links are now provided from articles in UKPMC to the corresponding record in a CRD database.  The example here provides a link from the UKPMC abstract through to the corresponding  record in the DARE  (Database of Abstracts of Reviews of Effects) database where the reader is informed that "apart from a relatively limited search, this was well-conducted and clearly-reported review, and the authors’ conclusions are likely to be reliable."

Currently, there are 11,658 links from UKPMC articles to DARE abstracts and 9,218 links from UKPMC articles to NHS EED (Economic Evaluation Database) abstracts.

Monday, 27 June 2011

Leading research organisations announce top-tier, open access journal for biomedical and life sciences

The Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust announced today that they are to support a new, top-tier, open access journal for biomedical and life sciences research.

The three organisations aim to establish a new journal that will attract and define the very best research publications from across these fields. All research published in the journal will make highly significant contributions that will extend the boundaries of scientific knowledge.

Read the full press release on the Wellcome Trust website.

Royal Society Medicine Open papers -- now deposited in PMC

Papers published under the Royal Society of Medicine's open access option (RSM Open) are now deposited in PubMed Central and mirrored to UKPMC.

The open access option is available to all authors and applies to all RSM journals.

The Article Processing Charge (APC) for RSM Open is $3000.  All papers published under this model are licenced using the Creative Commons Attribution, Non-commercial licence.

A list of all papers published under this model is available here.

Wednesday, 22 June 2011

Scientific Reports: a new open access journal from NPG

A new online open access journal from Nature Publishing Group, Scientific Reports, is now live.

The journal is a primary research publication covering all areas of the natural sciences.

The APC for UK articles has been set at £1,112 (from January 2012). Scientific Reports will apply to be indexed in all relevant databases and repositories, and all content will be archived in PubMed Central. More

Monday, 20 June 2011

UK PubMed Central is hiring!

We are looking to recruit experienced developers to join the Literature Services Team at the European Bioinformatics Institute (EBI) to help deliver UK PubMed Central. This is a great opportunity to contribute to a core resource for biomedical researchers.

The positions involve a range of activities, depending on where your experience lies. We require people who can demonstrate excellence in a variety of technical skills.

You can find out more about these vacancies on the EMBL wesbite.

Wednesday, 8 June 2011

The Power of Text Mining

Text mining features in databases are an increasingly popular way to extract useful information that could otherwise remain hidden. A new resource has become available to allow researchers to search for particular chemical compounds in biomedical literature. This task is often confounded by multiple names for particular chemicals being used in publications. Similarly, sometimes the structure may be known but the investigator may lack a name for the compound. Compounds In Literature (CIL) helps overcome these problems, via a novel web interface, helping researchers to locate chemical names, structures, or even similar structures in over 28 million compounds of PubChem and more than 20 million citations from PubMed.

“CIL-results provide a ‘heat map’-like overview, comprising compounds, similar compounds, proteins and citations with highlighted found entities….CIL allows for analyses of obvious and hidden potential biological functions of compounds.”

Like UKPMC, the CIL service uses EBI’s 'Whatizit' tool, in this case to locate related compounds, proteins and citations. Similarly, UKPMC searches for synonyms of keywords (named entities) and can capture many articles or content that may not be picked up by other resources. This capability is just one aspect of the powerful text mining features available to UKPMC users. Further information on text mining in UKPMC is available in the FAQ section.

Wednesday, 4 May 2011

Open Biology: an open access journal from the Royal Society

Competition in open access publishing is increasing with the launch of two similarly named online open-access journals. Open Biology (Royal Society Publishing) will start receiving submissions this July whilst Biology Open (BiO; The Company of Biologists), discussed in the previous post, is set to launch in the autumn of 2011. Like BiO, Open Biology will cover a broad range of subject areas from cellular biology, immunology and neuroscience to microbiology and genetics. The article processing charge of the latter has been set at £1200 (€1560) to cover costs, although authors in developing countries can take advantage of waivers to reduce this charge. Published articles will be available free in PubMedCentral and UKPMC. Neither journal should be confused with the existing title ‘The Open Biology Journal’ (Bentham Open).

Tuesday, 3 May 2011

Biology Open: a new OA journal from the Company of Biologists

The Company of Biologists has announced BIOLOGY OPEN (BiO), a new online only, Open Access journal publishing original research across all aspects of the biological sciences including cell science, developmental biology and experimental biology. 

Launching in Autumn 2011, BiO aims to "provide rapid publication for peer reviewed, scientifically sound observations and valid conclusions in these allied fields.  By focusing on the timely publication of sound research rather than that with perceived impact or importance, Biology Open is designed to facilitate dialogue and build a valuable body of work supporting the efforts of the research community.  The impact of each paper will be decided by the community through usage and discussion.  

The journal will also consider useful reports of negative results.  Authors will be able to submit direct or benefit from our manuscript rapid-transfer system if their original submission was to one of The Company of Biologists’ flagship journals, DevelopmentDisease Models & MechanismsJournal of Cell Science and The Journal of Experimental Biology".

The APC for articles which are published in BiO has been set at $1,350.  Accepted papers will be deposited in PMC at the time of publication and mirrored to UKPMC.

Thursday, 28 April 2011

AAI offer a free manuscript deposition service to PMC/UKPMC

The American Association of Immunologists, publisher of The Journal of Immunology, have launched a new, free service to authors, to deposit selected manuscripts to PubMed Central (PMC).  Articles deposited in PMC are automatically mirrored to UKPMC.

"Several funding bodies, including the National Institutes of Health, Howard Hughes Medical Institute, Wellcome Trust and Medical Research Council, mandate that authors deposit published articles into PMC or UKPMC.  While these mandates apply to authors, not publishers, the new AAI service will help authors comply with these mandates.

On behalf of authors who are funded by such bodies, AAI will deposit all manuscripts that begin submission to The Journal of Immunology after March 29, 2011 and are ultimately accepted for publication; the author must select this option on the online submission form in order for AAI to do so.  AAI will deposit the version of the manuscript that has undergone peer review and has been accepted for publication, before copyediting and formatting".


All UKPMC funders mandate that articles be made available to the public in PMC at 6 months after publication; manuscripts deposited by AAI will comply with thus embargo period.

Tuesday, 26 April 2011

Increasing amount of content in UKPMC is fully open access

Analysis of the content in UKPMC shows an increasing proportion of articles are fully open access and thus can be downloaded, and re-used, typically for non-commercial purposes.  To be clear, all content in UKPMC can be accessed without any restriction, but only a subset of this content is fully open access.

In 2001, just 7% of the articles published in that year and added to UKPMC, were defined as "open access".  [35,061 articles, with a publication year equal to 2001, were added to UKPMC, of which only 2,543 were open access.]

In 2009, 33% of the articles published that year and added to UKPMC were classified as "open access". [125,592 articles, with a publication year equal to 2009, were added to UKPMC, of which  41,811 were fully open access.]

The graph below shows the growth of open access articles in UKPMC between 2001 and 2009.



Open access articles in UKPMC: 2001 and 2009

Open access articles are still protected by copyright, but are made available under a Creative Commons or similar license that generally allows more liberal redistribution and reuse than a traditional copyrighted work. 

Crucially, because these articles can be downloaded without restrictions, users can deploy text mining tools to crawl this corpus of literature to help identify new facts and knowledge.

The open access articles in UKPMC can be downloaded from the UKPMC FTP site.  This site is updated weekly.

Thursday, 7 April 2011

Heading for the Open Road: costs and benefits of transitions in scholarly communications


A report published today looking at how to improve access to academic literature suggests that open access is likely to have the greatest benefits to the UK scholarly communications system.

Open access, whereby research outputs are made freely accessible to the widest possible audience, is an issue to which the Wellcome Trust is firmly committed. The Trust provides funding to its researchers to cover open access publishing costs.

'Heading for the Open Road', a new report commissioned by the Research Information Network and other funders, including the Trust, supports this approach. It discusses a number of scenarios and suggests that the "Gold" scenario - the model in which author-side payments are levied to enable immediate open access to the published article - has the potential to achieve the highest benefit-cost ratio while lowering the UK's net costs for scholarly communication. It is also the only model that is considered to be fully sustainable.

However, the report also makes clear that there are risks associated with this approach, as the scale of the costs and benefits depends on the future level of charges levied on the author, which it may be hard for policy makers to influence. Moreover, there are likely to be significant challenges in the transition to this approach (possibly more so than in other scenarios), including the one-off costs to create the necessary systems and infrastructure, and the lags that mean ongoing net costs could rise before later falling because of the need to meet author-side payments while retaining existing subscription journals.

Sir Mark Walport, Director of the Wellcome Trust, says: "This report shows that financial savings to the UK - and particularly UK academic institutions - can be realised if an 'author pays' publishing model is implemented effectively. This is a challenge and an opportunity to the best publishers of scholarly journals."

Image: The open road, by Dr DAD on Flickr.

Monday, 28 February 2011

BMJOpen launched

BMJ Open - BMJ's new online-only, open access journal - has been launched. The journal will publish "all research study types, from study protocols to phase I trials to meta-analyses, including small or potentially low-impact studies".

In a move to promote greater transparency in the peer review process, all published articles include the reviewers reports, responses from the author and (where necessary) a further commentary by the reviewers.  All reviewer reports include details of who has undertaken the review (name, affiliation, and contact details.)

The article-processing charge for papers accepted for publication is £1200.

All published articles are deposited in PMC and made available in UKPMC.  Articles are licenced under the Creative Commons, attribution, Non-commercial licence.

Publication in BMJ Open meets the open access requirements of the Wellcome Trust and the other members of the UKPMC Funders Group.

Tuesday, 22 February 2011

Wellcome Trust and the author-pays model

A presentation by Robert Kiley (Wellcome Trust) given at the annual conference of the Association of Subscription Agents and Intermediaries that looks at the Wellcome Trust experience with the author-pays, open access model.

Looking at Wellcome-funded papers published in the quarter of 2010, Kiley calculates that the average cost of papers published under the author-pays model -- either through a hybrid or full open access option - was $2,367.

Based on this average fee, Kiley estimates that if every Wellcome-funded paper was routed through a "gold" OA route -- and assuming that the Trust picked up 100% of these costs -- then the total cost per year would be around $10.8m, which equates to around 1.25% of the Trust's annual research spend.

Wednesday, 2 February 2011

Wiley announce launch of new Open Access journals

Wiley have announced the launch of Wiley Open Access, a new publishing programme of open access journals.  The first three titles - Microbiology Open, Brain and Behavior and Ecology and Evolution - will all launch later in 2011.

Wiley Open Access journals will be published under the Creative Commons Attribution Non-Commercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.  All articles will be deposited in PubMed Central and UKPMC.

A publication fee will be payable by authors on acceptance of their articles, though the press release does not indicate what the fee will be.

This announcement comes hot on the heels of other publishers announcing their new open access journals including Scientific Reports (NPG), BMJOpen (BMG) and SageOpen (Sage).

Saturday, 15 January 2011

NPG announce plans to launch a fully Open Access journal

Nature Publishing Group (NPG) have announced that they will be launching a fully open access journal  - Scientific Reports - in July 2011.


Funded entirely through article process charges ($1350 per published article), Scientific Reports will publish "original research papers of interest to specialists within a given field in the natural sciences.  It will not set a threshold of perceived importance for the papers that it publishes; rather, Scientific Reports will publish all papers that are judged to be technically valid and original. To enable the community to evaluate the importance of papers post-peer review, the Scientific Reports website will include most-downloaded, most-emailed, and most-blogged lists. All research papers will benefit from rapid peer review and publication, and will be deposited in PubMed Central."


Authors who publish in this journals will be given the choice of  two Creative Commons non-commercial licenses (attribution, non-commercial, no-derivatives, or attribution-non-commercial-share-alike).


Other publishers who have also announced new OA journals include Springer (SpringerOpen), BMJPG (BMJOpen), Sage (SageOpen) and ASM' (mBio).