UK PubMed Central Blog

Open Access, UKPMC and PubMed: how are we doing?

2012-01-24T08:10:00.004Z

The graphic above shows articles available in UK PubMed Central (UKPMC) - read-only articles: green; Open Access articles: blue - compared to the number of abstracts in PubMed.

For articles published in 2010, using the ~925K articles in PubMed published in 2010 as 100%, UKPMC is about 18% of the size of PubMed, with Open Access articles around 7%.

A key factor to maintain this growth will be for the research community to improve compliance with the UKPMC Funder mandates, to ensure all articles resulting from those funds can be found in UKPMC.

Jo McEntyre
EBI/UKPMC

SpringerPlus -- new OA journal from Springer

2012-01-12T21:14:00.000Z

SpringerPlus, the new Open Access journal from Springer (and based on the PLoS One model) is now accepting manuscripts from all disciplines of science.

The journal will accept manuscripts describing original research as well as case descriptions and methods. The submission of data reports and large datasets is actively encouraged.

All articles accepted for publication will be published under the Creative Commons, Attribution (CC-BY) only licence, and be deposited by the publisher in PubMed Central/UKPMC. As such this journal is fully compliant with the policies of the Wellcome Trust and the other members of the UKPMC Funders Group.

Article Process Fess (APC's) are currently set at £700/$1085

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

2011-11-08T16:41:00.002Z

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.

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

2011-10-25T14:28:00.003+01:00

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)

Open Biology - a new open access journal

2011-10-17T15:53:00.005+01:00

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.

Mark Patterson named Managing Executive Editor of new open access journal

2011-10-11T16:50:00.000+01:00

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.

The Open Access Interviews

2011-09-02T16:58:00.000+01:00

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.

UKPMC is hiring!

2011-08-31T10:59:00.003+01:00

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.

European Bioinformatics Institute to lead UK PubMed Central

2011-07-29T09:25:00.003+01:00

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.

UKPMC Engagement Manager vacancy

2011-07-11T12:08:00.005+01:00

Engagement Manager

UK PubMed Central

British Library

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

2011-07-05T17:12:00.003+01:00

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.

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

2011-06-27T13:30:00.008+01:00

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

2011-06-27T11:27:00.001+01:00

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.

Scientific Reports: a new open access journal from NPG

2011-06-22T08:54:00.006+01:00

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

UK PubMed Central is hiring!

2011-06-20T15:27:00.003+01:00

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.

The Power of Text Mining

2011-06-08T14:28:00.007+01:00

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.

Open Biology: an open access journal from the Royal Society

2011-05-04T14:40:00.003+01:00

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).

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

2011-05-03T09:35:00.000+01:00

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, Development, Disease Models & Mechanisms, Journal 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.

AAI offer a free manuscript deposition service to PMC/UKPMC

2011-04-28T12:09:00.000+01:00

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.

Increasing amount of content in UKPMC is fully open access

2011-04-26T12:09:00.000+01:00

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.

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

2011-04-07T11:49:00.001+01:00

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.

BMJOpen launched

2011-02-28T13:48:00.000Z

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.

Wellcome Trust and the author-pays model

2011-02-22T23:28:00.002Z

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.

Wiley announce launch of new Open Access journals

2011-02-02T11:47:00.000Z

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).

NPG announce plans to launch a fully Open Access journal

2011-01-15T15:57:00.002Z

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).

UKPMC is Zotero-enabled

2010-12-22T15:49:00.001Z

Zotero is a free, easy-to-use research tool that helps you gather, organize, and analyze sources (citations, full texts, web pages, images, and other objects), and lets you share the results of your research in a variety of ways.

UKPMC is now "Zotero enabled", which means that users can store the bibliographic details of any UKPMC article directly into their Zotero Library. Items held in a Zotero Library can be exported as formatted references, tagged and searched. Figure 1, below, shows how to add a single item to your Zotero library.

Figure 1: Adding a single record to your Zotero library

When viewing a full text article (in html, not pdf) it is also possible to extract details of all the articles referenced in that article. (See Figure 2).

Figure 2: Adding multiple record to your Zotero library

Further information about Zotero - a extension to the popular open-source web browser Firefox - can be found at: http://www.zotero.org/

Eugenics Review : digitised and freely available through UKPMC

2010-12-06T17:27:00.001Z

The complete archive of the Eugenics Review journal - from 1909 through to 1968 when the title ceased - has been digitised through the Wellcome Library's Backfile Digitisation Project, and is now freely available at UKPMC and PubMed Central.

As the official journal of the Eugenics Education Society (later known as just the Eugenics Society) , the Review published papers written by prominent members of the eugenics movement, including Francis Galton, Julian Huxley and Major Leonard Darwin.

The Eugenics Society was founded to promote public awareness of eugenic problems, i.e. the existence of hereditary qualities both positive and negative, and the need to encourage social responsibility with respect to these qualities.

The Wellcome Library also holds the archives of the Eugenics Society.

Submission fees – a viable business model for Open Access publishing

2010-12-06T11:58:00.000Z

A new study commissioned by the Knowledge Exchange argues that there can be benefits to publishers if they switch to a model based on submission fees.

The report “Submission fees – A tool in the transition to Open Access?”, written by Mark Ware, concludes that this model could be particularly relevant to journals with a high rejection rate. They could combine submission fees with article processing charges in order to make the transition to open access easier.

The model has attracted interest but publishers regard the risks, particularly those involved in any transition, as outweighing the perceived benefits. To support any transition, funders, institutions and publication funds could explicitly allow submission fees as a cost as this is often unclear in their policies.

This new study draws on research (conducted SQW Ltd on behalf of the Wellcome Trust), which also concluded that submission fees could play a key role in helping publishers transition to an open access model.

When a publisher offer a Wellcome-compliant open access model (i.e. deposition of the final paper in PMC/UKPMC at the time of publication, and a licence which allows the work to be re-used), then publisher submission fees are an allowable expense.

UK PubMed Central report from NIHR 'trainee' meeting

2010-12-02T14:58:00.002Z

Over 240 National Institute for Health Research (NIHR) trainees recently attended the 4th Annual meeting at the Midlands Hotel in Manchester (November 30th - December 1st). Despite the freezing temperatures outside, the atmosphere inside was warm, welcoming and friendly.

The term ‘trainee’ is probably quite inappropriate, as it evokes the image of fresh young graduates. Here the trainees were a diverse group (doctors, dentists, midwives, statisticians, health economists and other allied health professionals). Many were senior fellows or clinical lecturers. We have all heard about working young doctors with long hours, but this group work exceptionally hard to manage a research programme alongside their professional duties on the wards and clinics.

Events were chaired by Professor Jim Neilson, NIHR Dean for Training and Dr Lisa Cotterill, Director of the NIHR Trainees Coordinating Centre. Delegates heard an upbeat assessment of the future of National Health Service (NHS) clinical research by Dr Russell Hamilton, Director of R&D for the Department of Health (DH). Despite the climate of economic uncertainty, the powers that be are convinced that clinical research will continue to be an important and protected activity for the NHS. Sir Iain Chalmers of the James Lind Library, delivered an inspiring lecture on evidence-based medicine and illustrated this with his moving personal experiences of Gaza in 1969/1970 and 2009/2010. Breakout sessions gave delegates the opportunity to discuss personal perspectives on managing a research career alongside clinical duties and focus on career development issues.

The meeting was attended on behalf of UK PubMed Central (UKPMC) by our newly appointed Engagement Officer, Dr Mohammed Tasab. Delegates were pleasantly surprised to learn of the range of useful tools and clinically relevant content available from the UKPMC site. The grant lookup facility and the availability of UK clinical guidelines were of particular interest to many participants.

In association with the other UKPMC funders, the DH and the NIHR is an important partner in the UKPMC initiative. They require that [for applications submitted from 1st April 2007] peer-reviewed research papers accepted for publication, and supported in whole or in part by DH/NIHR, are deposited at the earliest opportunity – and in any case within six months - in UKPMC.

Author: Mohammed Tasab

Window display to promote open access and UKPMC

2010-12-01T22:18:00.001Z

At the Wellcome Trust we are always keen to try new ways to promote our open access policy, and the UKPMC repository.

Our latest promotional activity involves a huge poster in the rear window (Gower Place) of the Wellcome Trust HQ, in London.

In addition to promoting OA, the poster also provides the opportunity for the Trust to promote its data sharing policy, and the work it is doing in providing access to the Library's collections, through its ambitious digitisation programme.

Almost 60% of Wellcome-funded papers in PMC are fully open access

2010-11-29T21:36:00.002Z

The Wellcome Trust's Open Access policy has always made it clear that it considers dissemination costs as legitimate research costs and as such provides grantholders with additional funding, through their institutions, to cover open access charges.

In view of this I thought it would be interesting to see how many papers, attributed to the Wellcome Trust and available through PMC and UKPMC, were "fully" open access papers, in accordance with the Bethesda Principles.

In summary, this means research articles which:

were made available in PMC with no embargo
deposited by the publisher as "version of record" articles (i.e. excluding Accepted Author Manuscripts (AAMs)
included an article-level licence that permitted re-use.

To identify the number of "full" OA articles I ran the following search on PMC (on 29th November 2010)

"wellcome trust" [gr] 14748 articles
[This finds all articles in which the Wellcome Trust has been identified as a research funder]
Limit #1 to articles published in 2009 = 2483
[This includes "full" OA articles, as well as author manuscripts, and articles which were made available through PMC because the publisher makes all content available through this repository.]
Limit #2 to "open access" articles = 1436
[This limits the previous set to full OA articles, as described above.]

A simple test to validate that the articles are "full OA" is to check that these articles are included in the OA subset, and thus can downloaded in XML format. The syntax for this is: http://www.pubmedcentral.nih.gov/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc&identifier=oai:pubmedcentral.nih.gov:2654146 (simply replace the last 7 digits with any open access PMC ID to see the XML

Using the above strategy we can see that around 58% of these articles are fully OA (in accordance with the Bethesda Principles).

Full figures are shown below:

Number of full, Bethesda-compliant, OA articles: 1436 (58%)
Number of AAM's: 483 (19%)
Number of other Version of Record articles, but had no explicit re-use licence: 564 (23%)

Company of Biologists develop full open access option

2010-11-24T22:38:00.000Z

The Company of Biologists (COB) - publishers of Development and Journal of Cell Science - has developed an open access ("gold") option, which meets the requirements of the UKPMC Funders' Group.

For a fee of £1350, the COB will deposit the final version of the article in PubMed Central (at the time of publication) and allow these articles to be re-used in accordance with the Creative Commons Attribution, non-commercial, share-alike licence.

From January 2011, all content for Disease Models & Mechanisms will be Open Access. The Article Processing Cost (APC) for this title is also £1350 (plus VAT if applicable).

All authors now displayed in UKPMC search results

2010-11-12T09:28:00.002Z

In response to user feedback, the UKPMC search results page now displays all the authors associated with any published article.

Prior to this change, the search results page had shown just the first seven authors, with the full set of authors only being visible from the abstract and full-text views.

Further feedback on the UKPMC service is welcomed.

Article about UKPMC in Nucleic Acids Research (Database Issue)

2010-11-10T11:15:00.001Z

The January 2011 Nucleic Acids Research Database Issue includes an article by Jo McEntrye and others, that describes the UKPMC service and the developments which have taken place over the last three years.

Key developments include:

Single search: Through UKPMC a user can search across some 24 million bibliographic records drawn from PubMed, Patents and recent biomedical theses, as well as the 1.8 million full-text articles held in the UKPMC repository

Citation services: UKPMC contains ‘Cited By’ information as an alternative way to navigate the literature.
Text mining services. UKPMC has incorporated text-mining approaches to semantically enrich content and integrate it with related database resources.

Grantee services. Through UKPMC+ grantees can deposit manuscripts, link papers to grants, publish online portfolios and view citation information on their papers. .

The article also clarifies the relationship between PMC and UKPMC, providing historical context and future directions.

HTML version
PDF version
Screen version

NAR is in fully open access journal.

Open access at the Wellcome Trust: 5 years on

2010-11-02T15:52:00.001Z

In October 2006 the Wellcome Trust become the world’s first research funder to develop an open access policy that required the research outputs, that arose from its funding, to be made freely available. This presentation, delivered at the recent Berlin 8 meeting, reviews the progress that has been made over the past 5 years – in terms of compliance with the mandate, providing the infrastructure to support open access, and working with publishers to help them develop “Wellcome-compliant” publishing policies – and outlines what additional steps the Trust needs to take to help realise the full potential of its open access mandate.

Looking forward, the presentation also discusses the aspirations of the Wellcome Trust to transform UK PubMed Central into a single, Europe-wide repository for life-sciences research and, more generally, considers how research funders could help to influence innovation in scientific publishing in the open access arena.

View the presentation

UKPMC now offers search RSS

2010-11-01T15:01:00.001Z

By running a search through UKPMC, then clicking on the RSS feed logo once your search results have been displayed, you can add a search as feeds in a bookmark to your browser. When new journals are added to UKPMC, the updates will alter your search (remember to refresh your browser rather than used cached contents) - you just click through to the title you want to link through from the feed, accessible from your browser's bookmarks.

Author: Paul Davey

Links to chemical compounds now enabled

2010-11-01T14:48:00.000Z

As part of the text-mining work being undertaken by European Bioinformatics Institutue [EBI] and The National Centre for Text Mining [NaCTeM], it is now possible to get a list of all chemicals cited in a full-text article at UKPMC and link through to Chemical Entities of Biological Interest (ChEBI) database for further information.

By way of example, on viewing the article at http://ukpmc.ac.uk/abstract/PMC/PMC1828400 - and clicking on the Bioentities Tab - you will see that 11 chemical compounds have been identified.

In addition to chemical compounds, UKPMC articles are also linked to genes and proteins, protein interactions, species, and diseases.

FTP site for Open Access articles now available

2010-10-07T21:28:00.003+01:00

The Open Access subset of UKPMC articles - which as of October 7th 2010 contains around 195,000 full-text articles - can be downloaded via: http://ukpmc.ac.uk/ftp/oa

The content are available as 20 zipped files, named according to the PMCID range that each zipped file contains. The files are updated weekly.

UKPMC provides WoS citation counts

2010-08-20T09:57:00.007+01:00

UKPMC users can now view counts and link through to Web of Science citation data for articles available via the UKPMC website.

The UKPMC citations tab available on both the abstract and full text view of an article, already providing 'cited by' and 'cites the following' data, has been augmented by a WoS citation count, which links through to the full citation details on the WoS site.

Analysis of where Wellcome-funded authors publish: 2009 data

2010-07-01T16:48:00.018+01:00

An analysis of publication data for 2009 identifies a total 5263 Wellcome-attribured articles in PubMed, of which 2313 are freely available in UKPMC. This indicates an overall open access compliance figure of around 44%.

Looking at the data more granularly, we can also see which journals are most used by Wellcome-funded authors.

In total, some 1113 journals published Wellcome-funded research in 2009 -- from Acta Crystallographica through to Zoones and Public Health -- with the top 10 titles (in terms of total number of articles published) publishing some 14% (733 articles) of the total "Wellcome research output".

As can be seen from the image above (click on it to make it legible), PLoS One was the title most used by Wellcome-funded researchers, publishing a total of 136 papers in 2009.

Why use UK PubMed Central?

2010-07-01T15:04:00.001+01:00

You have probably used PubMed, or PubMed Central, the archive of full-text life sciences journals (both developed by the National Center for Biotechnology - NCBI, at the National Library of Medicine in the United States). Developed in close collaboration with NCBI, UK PubMed Central (UKPMC) offers, at its core, the very same as PubMed and PubMed Central - access to the widest range of free, peer-reviewed and quality assessed biomedical and health literature available anywhere. That equates to over 19 million abstracts and 1.8 million full text articles but they are brought together to search from one website.

In addition, UK PubMed Central provides a gateway to a wealth of unique additional content and innovative features which specifically support the UK researcher's information requirements.

What is different about UK PubMed Central?

It is not just about the range of literature available, currently 23,661,932 items (as at 22.06.2010), it is also the clarity and ease of use of the interface, the innovative and practical features available to you, and the links to potentially relevant sources of information which have been peer-reviewed and quality-assessed, that make UKPMC unique.

Additional content

As well as access to the entire content of PubMed, UKPMC offers links to additional content sets and databases. You can download more than 2,700 National Health Service clinical guidelines; search for almost 2 million patents; and look-up more than 20,000 PhD theses. For those with an interest in agriculture, UKPMC even offers access to Agricola, the United States Agricultural Library database.

An Interface and functionality developed in consultation with the research community

All our developments have been undertaken following iterative, collaborative consultation with biomedical and health researchers from across the UK. Through focus groups, workshops, online surveys and face-to-face consultations we have developed an interface that is intuitive, clear and easy to navigate.

Practical features and tools to support your research

As you search UKPMC, you can record all your searches. collate and email search results, and export citations into reference management software (RIS export format is supported). Other relevant articles are automatically highlighted as you search, and you can also broaden or narrow your search to other articles using our MESH subject indexing.

A breadcrumb trail: taking you to further relevant, peer-reviewed sources of information

When you find a research article of interest, and click through to it, UKPMC may also provide you with links, where available, to other sources of information gleaned from terms found within abstracts or the full text of articles you have downloaded. You can tick checkboxes to highlight key terms such as - Gene Ontology; Genes/ Proteins; Species - or you can also link to further sources of information such as biological entities, or to papers cited by the article (and, when available, also find out who has cited the article).

It is our aim to improve the UKPMC Beta service so it benefits you and your research needs. We welcome any feedback you may have. Please email us at or click the feedback button on our website.

Author: Paul Davey

UKPMC Beta service moves into production

2010-06-22T15:30:00.008+01:00

As of Wednesday 23rd June, the UK PubMed Central (UKPMC) Open Beta site will go into full production mode, replacing the 'Classic' service available at http://ukpmc.ac.uk.

Unveiled at a showcase event at the British Library earlier this year, the UKPMC Beta site provides users with a single point of access to:

1.8 million+ full text, peer reviewed published journal articles covering all fields of biomedical and health research (the UK PubMed Central repository)
19 million+ PubMed abstracts
National Health Service (NHS) clinical guidelines
UK biomedical and health PhD theses
European Patent Office Patents, Agricola, Chinese Biological Abstracts and Citeseer databases

This content is made available to users via a completely redesigned user interface, which provides citation and full-text search; quick retrieval of relevant content; facetting of results; 'cited by', 'cites the following', 'biological entities' and 'related articles' links for journal articles and a full range of clipboard and export options.

In addition, the site has begun to integrate text-mining services which highlight and link biological entity types - currently gene/protein interactions, gene ontology terms, species, drugs and diseases - found within the text of an article to relevant external data sources.

Whilst of production quality, these services are still in development - for the UKPMC Beta site with its current functionality is an interim deliverable of a three-year programme of work which runs until June 2011. Over the next 12 months the UKPMC site and its services will continue to evolve. More information about this programme is available on the UKPMC website.

***

UK PubMed Central is a service of the UKPMC Funders Group working in partnership with the British Library, University of Manchester and the European Bioinformatics Institute in cooperation with the National Center for Biotechnology Information at the U.S. National Library of Medicine (NCBI/NLM).

98% of articles in PMC accessed in one year

2010-06-09T13:35:00.006+01:00

At a recent PubMed Central National Advisory Committe meeting, David Lipman (Director of NCBI) gave a presentation on the current status of PubMed Central which included the following data:

Over 1.9 million articles are available in PMC. (Expected to hit 2 million by end of June '10);
Participating journals: 640 full participants; 220 that participate through the NIH Portfolio; 880 titles who provide "selective deposit" to PMC (i.e. through author-pays model);
In a single month (March 2010) over 20 million articles were downloaded;
Over a period of 12 months (2009) 98% of content in PMC was accessed at least once; 69% of the articles were accessed 10 times or more (see image above).

Karger offer "Wellcome-compliant" OA option

2010-06-07T14:51:00.008+01:00

Karger Publishers have introduced an open access option, known as "Author's Choice".

In return for a fee of CHF 3,000, Karger will make an article freely available (at the time of publication) through http://www.karger.com/ , as well as depositing the final version directly into PubMed Central.

Articles routed through this mechanism are licenced under the Creative Commons, Attribution, Non-commercial licence. For further details see: http://content.karger.com/services/choice.asp

This Author Choice option meets the requirements of the Wellcome Trust and the other funders in the UKPMC Funders' Group.

ASM launches open access journal

2010-05-25T20:48:00.004+01:00

The American Society for Microbiology have launched a full online only, open access journal, known as mBio.

In an attempt to "break away from the current publication model", mBio editors will "either accept or reject manuscripts and will request only minor revisions; editors generally will not require authors to make extensive modifications or perform additional experiments. mBio's streamlined decisions do not mean less rigorous peer review, however. mBio editors, invited editors, and external referees are all active working scientists who are in the best position to judge the quality and importance of the work."

Another innovative development is the requirement for authors to explain, in plain English ,why the work is important. mBio editors hope that this development "will allow the importance of the work to be appreciated by nonspecialist scientists and critical nonscientific audiences, such as lay media, policy makers, and the general public." An example of this feature can be seen here.

All articles published in mBio are licenced under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported license.

The publication fee (article process charge) is $2000 for ASM members and $3000 for non-members.

All articles will be made freely available from UK PubMed Central and PubMed Central.

Transparent OA pricing policy from the Royal Society

2010-05-20T08:47:00.003+01:00

The Royal Society has announced plans to develop a transparent pricing policy in which the subscription cost of its journals are linked to the uptake of author-pays, open access articles.

"From 2012 we shall implement a new and more transparent pricing policy in which the price of each journal is tied to the number of non-open access articles published in that journal and each journal will publish the relevant article counts annually. We recognise the legitimate concerns of the research community that publishers of hybrid open access journals should take full account of the income they receive from article charges when setting subscription prices and believe that this model represents a coherent and viable way forward."

Further details of the Royal Society's open access publishing option (known as EXiS) can be found here.

See related post: Wellcome Trust calls for greater transparency from journals on open access publishing costs

Open access costs and benefits for universities: report available

2010-03-22T14:48:00.004Z

Open Access can offer universities real cost saving benefits, claims Alma Swan in a report - 'Modelling Scholarly Communication Options: Costs and Benefits for Univeresities', published in February 2010 (download here: http://ie-repository.jisc.ac.uk/442/).

Swan claims that the move to Open Access can 'disrupt systems and processes that have been in place for a very long time' (page i, Executive Summary) but the report makes it clear that it will be worth the effort, economically, in the longer term. 'Academic returns help in outweighing the price of change'.

The report includes analysis of the savings that could be made (or losses incurred) when adopting different OA routes, but in general argues the case for there being many advantageous cost savings to be made. One extremely important aspect for the researcher is the potential for OA to increase visibility, which 'translates into a high level of usage, measured by the number of downloads from repositories or from publishers' websites wherever articles are provided through these website in an openly accessible way' (p.58).

European research funders throw weight behind UK open access repository

2010-03-01T08:45:00.008Z

Four European research funders have today added their support to the open access repository UK PubMed Central (UKPMC) by agreeing that the life sciences research outputs made possible with their funding are made freely available through this repository.

Launched in January 2007, UKPMC is a free-to-access digital archive of full-text, peer-reviewed biomedical and life sciences research. As of February 2010, it holds over 1.7 million full text articles. The ambition of the repository is to become the information resource of choice for the UK biomedical and health research communities and eventually to expand to become 'Europe PubMed Central'.

Today, this aim takes a step closer as four European research-funding organisations - the Health Research Board Ireland and Science Foundation Ireland, Telethon Italy and the Austrian Science Fund - have agreed to participate in UKPMC. The funders will mandate that all biomedical research outputs that arise from their funding are made freely available - typically within six months of publication - from the UKPMC repository.

The development has been welcomed by Sir Mark Walport, Director of the Wellcome Trust, one of the principal funders of UKPMC: "Free access to peer-reviewed research is essential for facilitating progress in biomedicine. I am delighted that these European funders have thrown their support behind UKPMC, and hope that other European research funders will follow their example. This should enable us to build on the success of the repository and expand to a Europe-wide service."

The four European funders will take part in 'Phase I' of UKPMC, and as such will be provided with a fully-managed repository service, along with a manuscript submission system to allow their researchers to archive their papers in the UKPMC repository. Access to the Grant Reporting System is also enabled, allowing researchers to report on the outputs of their grants.

Lucia Monaco, Chief Scientific Officer, Telethon Italy, commented that "as a charity funded by patients, we are excited about the opportunity to make the primary outputs of our research freely available to scientists, patients, donors and the general public through UKPMC. The world-wide visibility offered by UKPMC through its connection to PMC and the European prospect it offers have made it the repository of choice for Telethon-supported publications".

Funders will also benefit from the developments being made to the UKPMC service. Key developments include providing the functionality - through text and data mining technologies - to integrate research articles with a range of other online sources, such as gene, protein and chemical compound databases, and to integrate a range of bibliographic databases - including Medline, Patents and Agricola - into a single, seamless discovery tool.

Phase I funding is based on a simple 'pay-as-you-go' model in which a small fee is charged for each author manuscript that is deposited in the UKPMC repository (to cover the cost of converting a manuscript to XML). All ongoing infrastructure costs will continue to be met by the existing UKPMC funders.

It is anticipated that Phase I will run until Summer 2011, to be followed by Phase II, a fully fledged Europe PubMed Central with a range of additional, value-added services.

Raising compliance with UKPMC Funders’ OA mandates: action plan

2010-02-16T09:48:00.006Z

The Wellcome Trust, on behalf of the UKPMC Funders’ Group, held a workshop in September 2009, for HEI repository managers and research/open access administrators, to discuss the issues involved in ensuring that funder open access mandates are met.

Prior to the workshop, a questionnaire was distributed to delegates, to identify the different barriers (and the most important of these) which prevent adherence to the mandates.

The results of the survey were summarised during the workshop and then delegates broke into groups to develop actions around the main themes of :

Accessing funding
Communication
Monitoring compliance
Messages for publishers

The actions generated from these groups form the basis of a joint action plan, which comprises three ‘mini’ action plans: one for funders, one for institutions and one for publishers.

The UKPMC Funders’ Group will take overall ownership of the further development and implementation of these plans and will work with institutions and publishers to do this, through a new ‘Institutions’ Panel’ and a reconvened ‘Publishers’ Panel’.

The Insitutions' Panel is now being established by the Wellcome Trust. The inaugural meeting will be in April or May 2010 and it is likely that the panel will meet twice a year. Any repository managers or research/open access administrators who support researchers funded by UKPMC funding organisations who are interested in finding out more about this panel, or who would like to join, are invited to contact the Wellcome Trust, in the first instance, at openaccess@wellcome.ac.uk.

Maney Publishing Group develops Open Access option

2010-01-15T14:33:00.002Z

Maney Publishing have developed an author-pays option for around 40 of their journals, including 15 titles in the health sciences with the intention to expand this to humanities journals in the future.

In return for paying a fee of US$2,000/£1,250 Maney will deposit the final version of the article directly to PMC (and other repositories as nominated by the author).

Articles published under the MORE OpenChoice option will be licenced using the Creative Commons, Attribution, non-commerical licence. Further details are available on the Maney web site.

This OpenChoice option meets the requirements of the Wellcome Trust and the other UKPMC Funders

Innovative new web interface improves access to UK’s largest free online life sciences resource

2010-01-11T13:02:00.005Z

The British Library have issued a press release to announce the launch of the new UK PubMed Central Open Beta website at beta.ukpmc.ac.uk:

Helping researchers access and exploit over 1.7 million full-text, peer reviewed biomedical research articles and over 19 million other life science research papers, on 12 January the British Library will showcase a whole range of new search and data mining tools designed to unlock the scientific knowledge held by UK PubMed Central.

Developed in direct consultation with researchers, UK PubMed Central (UKPMC) aims to become the information resource of choice for the UK biomedical and health research community. Launched by Professor Dame Sally C. Davies, Director General, Research and Development at the Department of Health, the Open Beta version of UKPMC will enable researchers to search and link information from literature and drill down into underlying datasets in new and innovative ways.

Supported by the UK's eight principal funders of biomedical and health research, who fund over 90% of the country's research publications in the field, UKPMC offers users a comprehensive and sustainable repository for UK funded free-to-access life sciences research. Developed in collaboration with the founders of PubMed Central in the US, the National Centre for Biotechnology Information (NCBI), the consolidation of published research outputs into globally accessible resources such as UKPMC is not only vital for widening access to knowledge and improving the efficiency of desk research, but it will also vastly improve the ability of funding organisations to assess the impact of their research, and help to better inform scientific strategy and policy making.

The showcase event will provide the chance to try out some of the new features that have been developed by the British Library and the consortium of programme partners including European Bioinformatics Institute, Mimas at the University of Manchester and the National Centre for Text Mining. There will also be the opportunity to hear from some of the key funders behind the programme, including Professor Doug Kell, Chief Executive of the Biotechnology and Biological Sciences Research Council, and Sir Mark Walport, Director of the Wellcome Trust, on the value and importance of UKPMC for the research community.

The easy-to-use, intuitive interface developed by the British Library for the latest Beta version will enable researchers to:

Conduct a full-text search of 1.7 million articles
Access abstracts for over 19 million articles
Exploit the scientific literature with innovative features which enrich abstracts and full-text articles by linking scientific terms to other sources of quality assured and useful information
Search content not included in traditional journal literature – including clinical guidelines as well as other hard to find material such as PhD theses

Professor Dame Sally C Davies – Director General Research and Development Department of Health said:

“I am delighted that UK PubMed Central is ready to launch new features on its website. This technology will make it possible to discover and use hidden ‘gems' of information buried in the documents within UK PubMed Central. The Funders' commitment to Open Access, and to making research outputs available through UK PubMed Central, means this advance will increase the knowledge base and allow research to realise even greater health and economic benefits for this country.”

Richard Boulderstone, the British Library's Director of eStrategy, says:

“With over 1.7 million full-text, free-to-access biomedical research articles and an ever increasing archive of additional research content, such as PhD Theses and Clinical Guidelines, UK PubMed Central is fast becoming the information resource of choice for the UK's biomedical and health research community. Developed by the British Library through open consultation with a wide range of researchers, the new data mining tools will allow users to really interrogate the collection; informing research, reducing duplication of work, and inspiring new scientific discovery.”

For more information and interviews please contact the British Library Press Office - Jacob Lant jacob.lant@bl.uk / +44(0)20 7412 7105 or Miki Lentin miki.lentin@bl.uk / +44(0)20 7412 7112.
Notes for Editors

1. UK PubMed Central ( www.ukpmc.ac.uk ) is a UK initiative of PubMed Central, the free archive of life sciences journals developed by the National Institutes of Health National Centre for Biotechnology Information (NCBI). NCBI is based at the National Library of Medicine in the United States. Read more on PubMed Central's international initiative here: http://www.pubmedcentral.nih.gov/about/pmci.html

2. UK PubMed Central mission is to become the information resource of choice for the UK biomedical and health research community by:

Establishing and expanding a single sustainable repository for UK-funded research outputs

Developing innovative tools to enable better and more effective use of the existing content

Providing access to additional content that integrates seamlessly into the UK PubMed Central web-site

Creating comprehensive analysis and reporting tools for researchers and funders to inform strategy and policy making

3. UK PubMed Central is supported with funding from:

• The Arthritis Research Campaign is the leading authority on arthritis in the UK, conducting scientific and medical research into all types of arthritis and musculoskeletal conditions. It is the UK 's fourth largest medical research charity and the only charity solely committed to funding high quality research into the cause, treatment and cure of arthritis, which affects more than ten million people in the UK today and millions more worldwide. We rely entirely on public donations to fund our research and education programmes, and spend more than £30m a year in universities and medical schools to support pioneering biomedical research in order to improve the lives of people with arthritis.

• The Biotechnology and Biological Sciences Research Council (BBSRC) is the UK funding agency for research in the life sciences. Sponsored by Government, BBSRC annually invests around £450M in a wide range of research that makes a significant contribution to the quality of life for UK citizens and supports a number of important industrial stakeholders including the agriculture, food, chemical, healthcare and pharmaceutical sectors. BBSRC carries out its mission by funding internationally competitive research, providing training in the biosciences, fostering opportunities for knowledge transfer and innovation and promoting interaction with the public and other stakeholders on issues of scientific interest in universities, centres and institutes.

• British Heart Foundation is the nation's heart charity, dedicated to saving lives through pioneering research, patient care, campaigning for change and by providing vital information. But we urgently need help. We rely on donations of time and money to continue our life-saving work. Because together we can beat heart disease.

• Cancer Research UK is the world's leading charity dedicated to beating cancer through research. The charity's groundbreaking work into the prevention, diagnosis and treatment of cancer has helped save millions of lives. This work is funded entirely by the public. Cancer Research UK has been at the heart of the progress that has already seen survival rates double in the last thirty years. Cancer Research UK supports research into all aspects of cancer through the work of more than 4,800 scientists, doctors and nurses. Together with its partners and supporters, Cancer Research UK's vision is to beat cancer.

• Chief Scientist Office is part of the Scottish Government Health Directorates, which supports and promotes high quality research aimed at improving the quality and cost-effectiveness of services offered by NHS Scotland and securing lasting improvements to the health of the people of Scotland. CSO supports research initiated by the research community in Scotland and advises the Scottish Government on how research contributes to improvements in health and healthcare. CSO's research strategy "Investing in Research: Improving Health" sets out our aims for the next 5 years and features changes to give greater emphasis to funding experimental and translational medicine research and health services and health population research. CSO also aims to deliver value for money through partnerships with other funding agencies and to foster Scotland-wide working through the Scottish Academic health Services Collaboration.

• Department of Health - Through the National Institute for Health Research, the Department of Health supports research in the NHS in England, with a budget of around £900m in 2009/10. The development of the NIHR includes a series of measures designed to transform the health research environment. See www.nihr.ac.uk. The NIHR's mission is to create a health research system in which the NHS supports outstanding individuals working in world-class facilities, conducting leading-edge research, focused on the needs of patients and the public.

• Medical Research Council For almost 100 years the Medical Research Council has improved the health of people in the UK and around the world by supporting the highest quality science. The MRC invests in world-class scientists. It has produced 29 Nobel Prize winners and sustains a flourishing environment for internationally recognised research. The MRC focuses on making an impact and provides the financial muscle and scientific expertise behind medical breakthroughs, including the first antibiotic penicillin, the structure of DNA and the lethal link between smoking and cancer. Today MRC funded scientists tackle research into the major health challenges of the 21st century. www.mrc.ac.uk

• The Wellcome Trust is the largest charity in the UK. It funds innovative biomedical research, in the UK and internationally, spending over £600 million each year to support the brightest scientists with the best ideas. The Wellcome Trust supports public debate about biomedical research and its impact on health and wellbeing. http://www.wellcome.ac.uk

4. The development partners for UK PubMed Central are:
The British Library, Mimas and NaCTeM (National Centre for Text Mining) at the University of Manchester, the European Bioinformatics Institute.

5. 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. It includes: books, journals, manuscripts, maps, stamps, music, patents, newspapers and sound recordings in all written and spoken languages www.bl.uk/science

Open Access uptake prompts 9% price reduction for The EMBO Journal and EMBO Reports

2009-11-20T16:49:00.008Z

Nature Publishing Group (NPG) and the European Molecular Biology Organization (EMBO) have announced that the prices for site licence access to The EMBO Journal and EMBO reports will be reduced by 9% in 2010, reflecting the increased publication of Open Access content in 2008.

Only last month (October 2009) the Wellcome Trust called for greater transparency among publishers to counter the argument that access fees are being paid twice - once through subscriptions and again through publication fees.

This decision by EMBO/NPG to reduce subscription is clearly a step in the right direction, though in the interests of transparency it would be useful if publishers - as a first step - disclosed what proportion of their content was routed through the author-pays model.

PMC Canada

2009-11-03T13:53:00.004Z

PubMed Central Canada is now live.

PMC Canada is a partnership between the National Research Council’s Canada Institute for Scientific and Technical Information (NRC-CISTI), the Canadian Institutes of Health Research (CIHR), and the US National Library of Medicine (NLM)

PMC Canada is the second PMC International site to be established.

European Respiratory Journal - self-archiving option

2009-11-01T10:40:00.006Z

The European Respiratory Society, publishers of the European Respiratory Journal, have confirmed that they will shortly be amending their instructions to authors to add that Wellcome Trust (or other members of the UK PMC Funders Group) will be permitted to deposit a copy of the final, peer-reviewed author-supplied manuscript (before copy-editing and publication) in PMC 6 months from publication in a print issue.

This self-archiving option is compliant with the policies of all the UKPMC Funders.

Endocrine Society's open access option

2009-10-27T10:18:00.004Z

The Endocrine Society - who publish titles such as the Journal of Clinical Endocrinology and Metabolism and Endocrinology - have developed an open access option for Wellcome Trust funded authors.

"The Endocrine Society will offer authors supported by the Wellcome Trust the option of meeting the publication requirements of the Trust by paying for an open access option. The cost to authors would be $3,000. Upon receipt of payment, the final print version will be deposited in PMC for immediate open access. These articles will be licensed using the Creative Commons, Attribution, Non-commercial license 2.0. " Further information is available from the Instruction to Author's page.

Currently this option is only available to Wellcome Trust funded researchers.

Wellcome Trust calls for greater transparency from journals on open access publishing costs

2009-10-19T15:21:00.004+01:00

As Open Access Week 2009 gets underway, the Wellcome Trust has called for greater transparency among publishers to counter the argument that access fees are being paid twice - once through subscriptions and again through publication fees.

The call comes as the Trust announces a further £2 million to fund open access publication fees for its researchers over the next 12 months. The funds are part of the ongoing commitment to ensuring that the results of all Trust-funded research are made freely available online.

Sir Mark Walport, Director of the Wellcome Trust, comments: "We are deeply committed to ensuring that research outputs are accessible to the widest possible audience. We are committing £2 million over the next year to support our researchers to make this happen and will be working closely with other funders, publishers and the research community towards this aim."

Since 2005, the Wellcome Trust has made it a condition of funding that researchers are required to make any Trust-funded publications available within six months through UK PubMed Central (UKPMC), the UK's life sciences online archive. The Trust will meet publication costs where the publisher agrees to make articles freely available through UKPMC at the time of publication and to license these works in a way that facilitates re-use, subject to proper attribution.

In recent months, however, concern has been expressed by the research community that publishers are using open access fees as an additional revenue stream without making a concerted effort to adapt their business models. In other words, access fees are being paid twice, through subscriptions and through publication fees.

"We would like to see a commitment from publishers to show the uptake of their open access option and to adjust their subscription rates to reflect increases in income from open access fees," says Sir Mark. "Some publishers, for example Oxford University Press, have already done this and we would like to see all publishers behave the same way."

British Journal of Cancer -- new licence for OA content

2009-10-15T21:10:00.006+01:00

The British Journal of Cancer - owned by Cancer Research UK (CR-UK) - has chosen to implement the Creative Commons Attribution-NonCommercial-Share Alike 3.0 licence http://creativecommons.org/licenses/by-nc-sa/3.0/ for articles published under the BJC OPEN initiative.

This licence permits distribution and reproduction in any medium, provided the original author and source are credited. The licence does not permit commercial exploitation without specific permission.

This licence meets the requirements of the Wellcome Trust and the funders in the UKPMC Funders Group.

Open Access and Funder Mandates workshop

2009-09-26T06:47:00.009+01:00

The Wellcome Trust, on behalf of the UKPMC Funders’ Group, held a workshop on the 24th Spetember, for HEI repository managers and research/open access administrators, to discuss the issues involved in ensuring that funder open access mandates are met.

The workshop was split into two sessions. The morning session focussed on the practical aspects of supporting funder mandates, including discussions around the administration and funding of author-pays charges. The afternoon session provided an opportunity for attendees to preview some of the new developments to the UKPMC service - including grant reporting functionality and the UKPMC beta website.

The overriding aim of the day was to establish a joint action plan to ensure that institutions, responsible for administering the requirements of the funder OA mandates, have the full support that they need to do the tasks involved effectively.

Workshop disucssion groups were lively and generated many ideas for actions around the main themes of monitoring compliance, messages for publishers, communicating with researchers and managing payments. These outputs will be used by the Funders' Group to produce a draft action plan - which will be circulated to delegates (and made available via this blog) by the end of October 2009.

The workshop presentations are available to view below.

UKPMC Funders' policies (Robert Kiley, Wellcome Trust)

Case study: setting up an institutional fund (Bill Hubbard, University of Nottingham)

Managing OA payments: experience from the front line (Chad Pillinger, University of Cambridge)

Defining an action plan (Nicola Perrin, Wellcome Trust)

'My UKPMC': new grant reporting services (Alison Henning, Wellcome Trust)

UK PubMed Central Overview (Paul Davey and Ernie Ong, British Library)

Publisher policies and RoMEO (Bill Hubbard, Univeristy of Nottingham)

OASPA conference

2009-09-22T09:05:00.003+01:00

The first Open Access Scholarly Publishers Association (OASPA) conference took place in Lund between the 14-16th September 2009. The full set of presentations will be made available from the conference site within the next week or so.

Robert Kiley, from the Wellcome Trust, spoke about the Trust's open access policy, grantee compliance with the OA mandate, and what steps needed to be taken to achieve full OA for all Trust funded research papers. A copy of this presentation is provided below.

OA Wellcome Lund Sept09

British Jounal of Cancer - archive now available in UKPMC

2009-09-17T20:24:00.006+01:00

The full archive (1947 to date) of the British Journal of Cancer -published by NPG on behalf of Cancer Research UK - is now available in UKPMC. Current content is embargoed for 12 months, though articles routed through BJC Open are made available at the time of publication.

The archive was digitised through the Wellcome Trust/JISC/NLM Medical Journals Backfiles Project.

PMC Canada -- will launch in Autumn 2009

2009-07-16T15:48:00.002+01:00

The Canadian Institutes of Health Research (CIHR), the National Research Council's Canada Institute for Scientific and Technical Information (NRC-CISTI), and the US National Library of Medicine (NLM) have announced a three-way partnership to establish PubMed Central Canada (PMC Canada).

"PMC Canada is a powerful tool that will help researchers build upon one another's work and speed up the discovery and innovation process to address important health challenges," says Dr. Ian Graham, Vice-President of Knowledge Translation at CIHR. "It will provide quick and easy access to a much broader audience, increasing the value and application of CIHR-funded research."

PMC Canada builds on the successful PubMed Central (PMC) archive developed by the US National Library of Medicine and will join UK PubMed Central (UKPMC) as a member of the broader PMC International network. This network enables national versions of PMC to share content, and will make much of PubMed Central and UKPMC content accessible through PMC Canada.

The initial release of PMC Canada, to be available in fall 2009, will include a basic bilingual interface, a manuscript submission system for CIHR researchers and a bilingual help desk. An advisory committee of Canadian health researchers and other stakeholders will guide PMC Canada's future development.

American Association for Cancer Research - Manuscript deposition service

2009-07-09T20:46:00.004+01:00

The American Association for Cancer Research (AACR) - publishers of journals such as Cancer Research and Molecular Cancer Research - have announced the launch of their manuscript deposition service.

Designed to assist journal authors in meeting their funders' archiving mandates, authors of articles published in AACR journals can elect to have the AACR deposit their accepted manuscripts to PubMed Central or UK PubMed Central, thereby meeting the archiving requirements of the National Institutes of Health, Howard Hughes Medical Institute, Cancer Research UK, the Wellcome Trust and the Medical Research Council.

For authors that choose to take advantage of this service, AACR will upload the accepted version of the manuscript to the repository upon acceptance, with a release date of twelve months (for National Institutes of Health) or six months (for Howard Hughes Medical Institute, Cancer Research UK, Wellcome Trust, and the Medical Research Council) post-publication.

No fee is charged for this service.

Five minutes of your time to help us: take part in UK PubMed Central images survey

2009-06-23T09:56:00.005+01:00

UK PubMed Central development partners at the British Library invite life sciences researchers to take part in a short survey on images (takes no more than five minutes). The British Library project team, which manages development activities for UKPMC, and is specifically tasked with identifying additional, hard to find content to add to UKPMC, is keen to understand what types of images researchers would find useful for potential inclusion in the repository.

Take part in the UKPMC images survey

Nature Publishing Group allows data- and text-mining on self-archived manuscripts

2009-06-18T12:28:00.004+01:00

Nature Publishing Group (NPG) have announced the development of a licence that will explicitly permit academic reuse of archived author manuscripts.

"NPG supports reuse for academic purposes of the content we publish. We want the excellent research that we publish to help further discovery, and recognize that data-mining and text-mining are important aspects of that," said David Hoole, Head of Content Licensing David Hoole.

Under NPG's terms of reuse, users may view, print, copy, download and text and data-mine the content for the purposes of academic research. Re-use should only be for academic purposes, commercial reuse is not permitted. Full conditions are available on nature.com.

The re-use permissions apply to author manuscripts, of articles published in NPG's journals, which have been archived in PubMed Central, UK PubMed Central (UKPMC) and other institutional and subject repositories. The terms were developed in consultation with the Wellcome Trust, the leading biomedical research charity.

As a result, the full text and metadata of these NPG author manuscripts will form part of the UKPMC Open Access subset of articles. "The Wellcome Trust was keen to expand the Open Access articles available on UKPMC," continued Hoole. "We wanted to clarify the copyrights and terms of reuse for archived content, so that we could offer NPG author manuscripts for the UKPMC Open Access subset."

"The Wellcome Trust is supportive of NPG's efforts to make archived content more reusable," said Sir Mark Walport, Director of the Wellcome Trust. "This is an important development because it shows that reuse can be facilitated, independent of business model, for text-mining and academic research."

These articles will be accessible via the UK PubMed Central OAI service (UKPMC-OAI), an implementation of the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH). NPG's re-use terms will be included in the metadata of these archived manuscripts.

This development is the next step in NPG's support for self-archiving. NPG's License to Publish encourages authors of original research articles to self-archive the accepted version of their manuscript, for public access six months after publication.

Forty-three journals published by NPG offer a free Manuscript Deposition Service to help authors fulfil funder and institutional mandates for public access. NPG's Manuscript Deposition Service will deposit authors' accepted manuscripts with PMC and UK PubMed Central (UKPMC).

American Society of Hemtaology implements Wellcome-compliant author pays option

2009-06-10T13:31:00.005+01:00

The American Society of Hematology - publishers of the journal Blood - have developed a Wellcome-compliant author-pays option.

In return for a fee ($2000), ASH will deposit the final version of Wellcome-funded articles directly into PMC, where they will be made freely available at the time of publication. Further, special licensing language has been drafted to allow end-users of Wellcome-funded articles unrestricted access to these articles. All articles are mirrored to UK PubMed Central (UKPMC).

In order for ASH to deliver these articles to PMC, Wellcome funded authors must acknowledge explicitly in the text (i.e., Acknowledgement section of the article) of their research article that:

(a) the research in the article they authored was funded by Wellcome Trust
and/or
(b) their institutional affiliation with Wellcome Trust

Authors can find out more information about funded research access options for Blood during the manuscript submission process.

Currently, the special licencing language only applies to researchers funded by the Wellcome Trust.

Other funding organisations who wish their author-pays articles to be licensed in the say way should contact Blood.

Am J Hygiene and Tropical Medicine clarifies author pays option

2009-06-04T22:37:00.007+01:00

The American Journal of Tropical Medicine and Hygiene (AJTMH) - published by the American Society of Tropical Medicine and Hygiene - have clarified their author-pays option.

For authors who select the OA option (at a cost of $2500) the journal office will deposit the final version directly in PubMed Central and it will be made freely available at the time of publication.

These articles will be licensed using the Creative Commons, Attribution, Non-commercial license, which permits others to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that the original authorship is properly and fully attributed.

This policy is fully compliant with the requirements of all the UKPMC funders.

Journals compliant with Wellcome mandate

2009-06-01T16:13:00.000+01:00

At a poster session at the Open Repositories Conference 2009, Peter Millington (Technical Development Officer st Sherpa) presented data on the number of publishers/journals used by Wellcome-funded authors that offered a Wellcome-compliant OA publishing policy.

Taking a cohort of 3766 papers published in 901 different journals, Millington shows that potential compliance increased from 70% in 2006 to 87% in 2009. (i.e. 87% of articles were published in journals that had a Wellcome-compliant OA policy).

Millinton's analysis is based on a fixed cohort of papers, published in 2006. Analysis undertaken by the Wellcome on more recent publications (see Funder manadate presentation, slide 14) shows a potential compliance of around 95%, with actual compliance hovering around 35%.

To help Wellcome-funded authors determine the OA publishing policy of the most popular journals used by Wellcome-funded authors the Trust has produced a simple A-Z journal list. This list provides advice – at the journal title level – on how best to comply with the Trust’s open access requirements in a way that also meets the journals’ publishing policy.

As a result of the mandates

2009-06-01T13:55:00.006+01:00

This presentation (to run, see below), given at the Research Information Network / Repositories Support Project event on May 29th, 2009, includes some interesting facts and figures about UK PubMed Central as well as a providing a brief outline of some of the development activities being undertaken by the British Library and partners Mimas, the European Bioinformatics Institute and NaCTeM

As a result of the mandates

2009-06-01T13:51:00.002+01:00

View more OpenOffice presentations from Pauladavey.

Funder mandates

2009-05-29T09:37:00.001+01:00

Presentation given at the RIN/RSP conference Research in the Open: how mandates work in practice on the 29th May 2009.

The presentation looks at a number of funder open access mandates, with special reference to the Wellcome Trust's policy and its implementation. The presentation also considers the author-pays model and provides data on the level of compliance with the Wellcome Trust OA mandate.

OA Mandates May 2009

View more OpenOffice presentations from henninga.

Posted on behalf of Robert Kiley

Royal Society OA pricing model changed

2009-05-21T20:40:00.000+01:00

The Royal Society have announced a change in the pricing structure for its author-pays, open access model, known as EXiS Open Choice.

Responding to author feedback, EXiS fees will now be based on a per-article rate, rather than a per-page rate.

There are now two article rates:

Full research articles and reviews are priced at £2,600 ($4,420).

Shorter format articles are priced at the lower rate of £1,500 ($2,550).

Articles published under this model are automatically deposited in PubMed Central (and mirrored to UKPMC) and made available at the time of publication. These articles are licenced using the Creative Commons Attribution, Noncommercial License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited and this use is for non-commercial purposes.

New UKPMC Grant Reporting services – including citation data – now available

2009-05-21T17:30:00.001+01:00

Users of the UK PubMed Central Manuscript Submission System (UKMSS) are now able to use a new service - 'My UKPMC' - to report on the outcomes of any grant funded by any one of the UKPMC Funders' Group member organisations. Grantholders can export these grant reports not only in standard .csv and xml formats but also as publicly available web pages, which will update dynamically whenever a new publication is added to either PubMed or UK PubMed Central.

The service also provides grantholders with a “My Impact” report which shows the number of citations each paper has attracted. The citation count data – again updated dynamically so that it always shows the most up-to-date data – is provided by Thompson/Reuters Web of Knowledge (WoK). Users who have full access to the WoK service will be able to see details of the citing articles.

Over time we hope to provide additional metrics from other organisations, along with data such as number of downloads from the UKPMC repository.

Grant reporting using ‘My UKPMC’ : a step-by-step guide [PDF 8MB]

Any questions or comments? Contact the UKPMC Helpdesk by email at ukpmc@bl.uk or by phone on 01937 546699.

ASBMB - join PMC and UKPMC

2009-05-18T08:55:00.000+01:00

The American Society for Biochemistry and Molecular Biology (ASBMB) - publishers of the Journal of Biological Chemistry (JBC), Molecular and Cellular Proteomics (MCP) and the Journal of Lipid Research (JLR) have announced that they will make all their content freely available through the PMC and UKPMC repositories, with a 12-month embargo. [Previously ASBMB were only depositing NIH and "Author Choice" papers to PMC/UKPMC.]

Researchers funded by any of UKPMC Funders should continue to make use of the ASBMB "Author Choice" option. On selecting this option, papers are made available at PMC/UKPMC at the time of publication (no embargo), and are licenced using the Creative Commons, Attribution, Non-Commercial licence (CC-BY-NC). This licence allows uses to copy, distribute and transmit and adapt the work, subject to attribution and that it is undertaken for non-commercial purposes.

Author Choice papers are also included in the PMC OAI set, which allows users to download and harvest the content in XML format (e.g. see a recent JBC article in html and XML).

Society for Neuroscience offer manuscript deposition service

2009-05-14T09:30:00.000+01:00

The Society for Neuroscience (SfN) - publishers of the Journal of Neuroscience - now offer a manuscript deposition service for Wellcome Trust funded researchers.

Under this option, the Society will deposit the final author manuscript (i.e. the version that includes all changes that were approved following the peer review process) in UKPMC, where it will be made freely available six months after publication.

No fee is charged for this service.

This service is currently limited to researchers funded by NIH, HHMI and the Wellcome Trust.

Further information is available at the SfN web site.

American Psychological Association develops Wellcome-compliant OA option

2009-04-28T17:03:00.000+01:00

The American Psychological Association (APA) - publisher of titles such as Journal of Abnormal Psychology and Psychological Bulletin - have developed a Wellcome-Trust compliant author-pays model.

In return for paying an OA fee ($4000) APA will deposit on behalf of the author, the final, published version directly into PMC, where it will be mirrored to UKPMC.

Such papers will be licenced such that anyone may "access, download, copy, display, and redistribute this article or manuscript as well as adapt, translate, or data and text mine the content contained in this document", as long as this is done for non-commercial purposes, and proper attribution is given.

Upon submission to an APA journal, Wellcome-funded authors will be asked to identify their manuscript as being Wellcome Trust funded. If the papers is accepted for publication, Wellcome funded authors should complete this form (pdf) to ensure that APA journals will deposit the manuscript in PMC.

As of April 2009, this author-pays option is only available to Wellcome-funded researchers.

RCUK - further support for open access

2009-04-24T09:17:00.000+01:00

Research Councils UK (RCUK) have published an independent study commissioned by the Research Councils into open access to research outputs.

The purpose of the study was to identify the effects and impacts of open access on publishing models and institutional repositories in light of national and international trends. This included the impact of open access on the quality and efficiency of scholarly outputs, specifically journal articles. The report presents options for the Research Councils to consider, such as maintaining the current variation in Research Councils’ mandates, or moving towards increased open access, eventually leading to Gold Standard.

Welcoming the study, Professor Ian Diamond, Chair of the RCUK Executive Group said: "This excellent study sets out a way forward for the UK Research Councils in relation to open access, building on the extensive activities already supported through repositories such as UK PubMed Central and ESRC Society Today. The Research Councils look forward to working with their partners across the research community to consider the options."

In response to the study, the Chief Executives of the Research Councils have agreed that over time the UK Research Councils will support increased open access, by:

building on their mandates on grant-holders to deposit research papers in suitable repositories within an agreed time period, and;
extending their support for publishing in open access journals, including through the pay-to-publish model.

Resources for researchers now on UK PubMed Central website

2009-04-23T14:31:00.000+01:00

There is now a ' Resources and Media ' section on the UK PubMed Central website. So far this includes:

Focus group highlights - 2 minute streaming video
In late February members of the UK PubMed Central project team ran a focus group at the University of Oxford. 18 PubMed Central users attended, including researchers, technologists and librarians working within the biomedical and health communities. You can view a short two minute video which provides a quick insight into how we conducted the focus group and favourable comments from those that attended. Get in touch (email ukpmc-engagement@bl.uk ) if you would like information about future events, workshops and focus groups - at this stage we particularly want to engage with researchers - the views and comments of this target audience is vital to help feed into our development activities.

Vital information for biomedical or health researchers
Are you a researcher with a grant awarded by any of the UK PubMed Central funding organisations? If so, download and scrutinise the latest UK PubMed Central promotional leaflet. As well as containing vital information for you, it also includes a very brief overview of our development activities.

Journal of Visualized Experiments (JoVE) [update]

2009-04-17T14:47:00.000+01:00

Following a previous posting on the topic of JoVE, I am pleased to report that the publisher has developed a Wellcome Trust /UKPMC Funders Group-compliant, open access option.

"For articles published under Open Access, JoVE applies the Creative Common Attribution-Noncommercial license . Under this license, authors retain ownership of the copyright for their article, but authors allow anyone to download, reuse, reprint, distribute, and/or copy articles for non-commercial purposes, so long as the original authors and source are cited. No permission is required from the authors or the publishers. "

The OA option at JoVE costs $2000 per video (if it is made without the help of the JoVE video-production services) and $3000 per video, if JoVE video production services are required.

The Open Access articles are made freely available in PubMed Central and UK PubMed Central immediately after publication.

Further details are available at the JoVE site.

Add a UKPMC search box to your browser toolbar

2009-04-15T17:16:00.000+01:00

Simply click this button to add the UKPMC search plugin to your browser search toolbar.

Supported by Firefox 2+ and Internet Explorer 7 only.

Journal of Visualized Experiments (JoVE)

2009-04-08T22:41:00.000+01:00

The announcement that the Journal of Visualized Experiments - JoVE - has moved from an open access model, to a subscription-based model, has attracted much comment in the blogosphere, as can be seen from the postings at the Nature Network, and the Scholarly Kitchen blogs.

As a consequence of moving to a subscription service, content from JoVE at PMC and UKPMC is now embargoed for two years.

Conscious that this change in policy means that no researcher funded by any of the UKPMC Funders can seek publication in this journal - the maximum permissible embargo set by these funders is 6 months - the Wellcome Trust has spoken with JoVE's Editor-in-Chief to determine whether any alternative publishing options are available.

Though the details have not yet been fully worked out, it seems likely that JoVE will offer a "Wellcome-compliant" author-pays, open access option.

A Wellcome-compliant, author-pays, OA option, is one where the publisher deposits the final version of the paper (or video in this case) directly in PMC, and attaches a licence to the paper (video) which allows others to re-use this content. Publishers may impose conditions on users in relation to attribution (i.e. users must attribute the work in the manner specified by the author or licensor) and commercial use (i.e. specify that the work must not be used for commercial purposes).

When the details of the OA, author-pays option have been determined, this blog post will be updated.

UKPMC Twitter feed available

2009-04-03T16:44:00.000+01:00

UK PubMed Central is on Twitter at http://twitter.com/UKPubMedCentral - for now just tweeting blog posts and links to UKPMC Funders' Group-funded articles as they become available in UKPMC.

Open access licence: researcher opinion sought

2009-04-01T17:01:00.000+01:00

A learned society has offered the Wellcome Trust an open access, author pays option for researchers who seek publication in their journal. However, the licence they wish to attach to these articles is more restrictive than the Trust would normally require when paying an OA fee.

The purpose of this posting is to seek opinion from the research community on whether these restrictions will, in any way, limit a researchers ability to re-use this content.

Summary of relevant licence conditions

The relevant section of the licence is shown below, in italics

PMC or UKPMC mirror site users may access, download, copy, display and redistribute articles, as well as text and data mine content in articles for non-commercial purposes only, subject to the following conditions:

In the case of text-mining, User may incorporate individual words, concepts and quotes up to 100 words per matching sentence, whereas longer paragraphs of text and images cannot be used.

Users may not create derivative works (as defined in the U.S. Copyright Act, 17 U.S.C. §101 et seq.) based upon the documents.

The Wellcome Trust is seeking input from the research community to help determine:

A) Whether such a licence would impact on your ability to re-use and re-purpose this open access content.

B) If so, please give some examples of research activities that would be limited by this licence.

If you would like to respond to this issue, please use the comment function below or send an email to r dot kiley at wellcome dot ac dot uk.

Paying for OA publication charges - new report

2009-03-30T08:59:00.000+01:00

The Research Information Network and Universities UK have produced a guide [PDF] to provide advice on paying open access publication charges.

Recommendations are made for each of the key players involved in the scholarly communication chain - higher education institutions, publishers, funder and authors. With regard to authors (researchers) the report makes the following recommendations:

authors should make use of services such as the Directory of Open Access Journals, and consider the options for publishing their results in such journals.
authors should familiarise themselves with their funders’ policies and requirements, with the options and the arrangements available to them in their institutions for meeting the costs of publication in open access and hybrid journals and with the administrative arrangements to apply for such funds.
authors should ensure that they have access to the funds necessary to meet the publication fee, before they submit articles for open access publication.

The report has attracted a number of comments from the open access community, including Peter Suber and Stevan Harnad.

ACS Open Choice articles - now in PMC and UKPMC

2009-03-24T17:23:00.000Z

Papers published by the American Chemical Society (ACS) under their Open Choice option are now available in PMC and UKPMC. Currently around 110 papers - drawn from 20 ACS journal titles - are now freely available. These papers can be found by running the following search on UKPMC:

ACS Author Choice [filter]

All future papers published under this model will be made available through these repositories at the time of publication.

ACS Open Choice articles are fully open access in the sense that the licence [PDF link] allows users - for non-commercial research and education purposes - to "access, download, copy, display and redistribute articles as well as adapt, translate text and data mine the content...."

This model meets the requirements of the Wellcome Trust - and the other funders in the UKPMC Funders Group.

UK PubMed Central - enabling easier reporting on the outcomes of grants

2009-03-23T16:42:00.000Z

Users of the UK PubMed Central Manuscript Submission System (UKMSS) will soon be able to use a new service - 'My UKPMC' - to report on the outcomes of any grant funded by any one of the UKPMC Funders' Group member organisations. Grantholders will be able to export these grant reports not only in standard .csv and xml formats but also as publicly available web pages, which will update dynamically whenever a new publication is added to either PubMed or UK PubMed Central.

In advance of 'My UKPMC' going live - at the end of April 2009 - grantholders are able to use the current grants reporting service on UKMSS to link their publications with any existing grants awarded by UKPMC Funders' Group members. The step-by-step guide below shows how to do this.

Grant Reporting using UK PubMed Central – step by step guide [PDF 5MB]

Finding funder attributed papers in UKPMC

2009-03-19T20:02:00.000Z

Each of the eight funders associated with UKPMC has a Funders Home Page from which you can find all papers in UKPMC which are associated with any of these funding bodies.

In addition to be able to view these full-text articles, the article metadata can be exported in csv or xml. This metadata can also be sorted in various ways (author, title, date) and it is possible to limit the output to author manuscripts or publisher depositions.

As of today (19th March 2009) there are 5725 Wellcome-funded papers in UKPMC, of which 4289 (81%) are publisher, final-version articles.

The links here show all the papers in UKPMC associated with the Wellcome Trust, and those which have been added to UKPMC within the last 30 days.

First U.S. public access policy made permanent

2009-03-13T09:46:00.000Z

As reported by Jennifer McLennan (Association of Research Libraries) on the SPARC-OpenData mailing list:

2009 Consolidated Appropriations Act ensures NIH public access policy will persist

Washington, D.C. – March 12, 2009 – President Obama yesterday signed into law the 2009 Consolidated Appropriations Act, which includes a provision making the National Institutes’ of Health (NIH) Public Access Policy permanent. The NIH Revised Policy on Enhancing Public Access requires eligible NIH-funded researchers to deposit electronic copies of their peer-reviewed manuscripts into the National Library of Medicine’s online archive, PubMed Central (PMC). Full texts of the articles are made publicly available and searchable online in PMC no later than 12 months after publication in a journal.

The NIH policy was previously implemented with a provision that was subject to annual renewal. Since the implementation of the revised policy the percentage of eligible manuscripts deposited into PMC has increased significantly, with over 3,000 new manuscripts being deposited each month. The PubMed Central database is a part of a valuable set of public database resources at the NIH, which are accessed by more than 2 million users each day.

Bulletin of the History of Medicine: author-pays articles now in PMC

2009-03-11T12:59:00.000Z

Papers published in the Bulletin of the History of Medicine, for which an author-pays fee has been paid, are now flowing directly in PMC. These papers should be mirrored to UKPMC within the next 24 hours.

American Thoracic Society develops a compliant OA policy

2009-03-09T09:41:00.001Z

The American Thoracic Society - publishers of the American Journal of Respiratory and Critical Care Medicine, the American Journal of Respiratory Cell and Molecular Biology and the Proceedings of the American Thoracic Society - have modified their Open Access policy such that it is now fully compliant with the open access grant conditions developed by the UKPMC Funders.

ATS have agreed to deposit (on behalf of the author) final version papers directly into PMC, where they will be made freely available 6 months after publication. This policy applies to papers that have been accepted for publication in any ATS journal that has been funded by any of the UKPMC Funders.

To take advantage of this service, authors funded by any UKPMC Funders simply need to indicate their funding source on the ATS Copyright Form and provide the grant number and contact name on the title page of the manuscript.

Papers deposited under this policy are automatically mirrored to UKPMC.

This policy took effect in January 2009 and applies retrospectively to eligible articles published from June 2008.

Developing UKPMC

2009-03-04T21:19:00.000Z

The British Library - who, in collaboration with MIMAS, and EBI are responsible for managing the UKPMC service on behalf of the UKPMC Funders Group - have been busy over the last few weeks running workshops and other events to begin the task of alerting the life sciences research community (and soliciting their input) to the developments which will come online at UKPMC over the next nine months.

You can read a summary of these planned developments at the UKPMC site or, for a more independent view, see the recent posting by Frank Norman (Librarian at the National Institute of Medical Research) and Branwen Hide's comments on the Research Information Network (RIN) blog.

Open access option now available on European Journal of Human Genetics

2009-03-04T08:27:00.000Z

Authors publishing research in European Journal of Human Genetics (EJHG) can now opt to make their articles open access.

Read the full press release from Nature Publishing Group.

Company of Biologists and UKPMC

2009-03-02T21:29:00.000Z

The Company of Biologists (COB) - publishers of Development and Journal of Cell Science - has announced a new policy in which papers published by researchers funded by the Wellcome Trust or the Medical Research Council will be automatically deposited in PMC (and mirrored to UKPMC).

The Company of Biologists will deposit the final version of all Wellcome Trust / MRC funded articles, and make these available within 6-months of publication. No fee is levied for this service.

The COB also offer an author-pays option, in which papers are made available with no embargo. The Wellcome Trust is currently in negotiations with the COB to determine whether these articles will be licenced in ways which meets the requirements of the Wellcome Trust.

When more information is available, I'll post details in this blog.

**Update: 6th March 2009.
The COB has confirmed that the deposition policy applies to all funders who mandate deposition in PubMed Central.

COB will deposit UKPMC funder-attributed papers (e.g. Wellcome, MRC, BHF, CR-UK etc.) at PMC and allow these to be mirrored to UKPMC.

UK PubMed Central Blog - welcome

2009-03-02T20:49:00.000Z

UK PubMed Central(UKPMC) is the the UK's online digital archive of full-text, peer-reviewed research publications in the life sciences.

This blog has been created as a way of alerting researchers to:

new service developments at UK PubMed Central
changes to publisher policies in terms of open access and self-archiving
relevant news from the open access (OA) blogosphere

If there are any issues you would like to see discussed on this blog - or if you have any questions you have about UKPMC, or open access in general - then please post a comment on this blog.

Robert Kiley, Wellcome Trust