Thursday, 25 July 2013

Tracking Data Citations in Europe PMC

We are pleased to announce a new feature in Europe PMC that allows you to track data citations in the scientific literature. It is now possible to search for papers that cite database records for several core life science databases, such as the European Nucleotide Archive, ArrayExpress, and PDBe, as well as dataset DOIs used by, for example, Figshare and Dryad. 

As well as searching the Europe PMC website, RSS feeds can also be created to alert you when a particular dataset or data type has been cited. See the Europe PMC website for more information. The methods used to identify these data citations are reported in a recent PLoS One article, available in Europe PMC: http://europepmc.org/articles/PMC3667078.

The SOAP and RESTful web services also support these searches.

Your comments on this new feature are welcome. To find out more about new Europe PMC developments, bookmark this blog, or follow us on Twitter @EuropePMC_News

Thursday, 18 July 2013

New Europe PMC External Links Service: enabling access to more resources

In an exciting new development, Europe PMC now provides direct links from articles to relevant externally held information, and enables third parties to suggest relevant resources that enrich our existing content.

The External Links Service is a mechanism for people to publish links from articles in Europe PMC to related information or tools. It could be used to link databases, datasets, full text articles, community commentary or coursework too. If it is in scope for Europe PubMed Central and can be linked to sets of articles, then it is possible to participate.

Seven Mile Bridge, Longest of a Series of Concrete Bridges Linking the Florida Keys From the Mainland to Key West. The Bridges Form Part of the Overseas Highway, the Longest Over-Water Road in the World.
http://www.flickr.com/photos/35740357@N03/4727569782/in/photolist-8cL2MQ-e6hMSw-cLD41f-8cKYuh
The service has initially been made live with three providers:


- to find all articles that have a link to an external source, you can use the search syntax HAS_LABSLINKS:Y

The new External Links Service page gives further information about the service including 'Rules of Engagement' and what to next if you want to share links with us. The page can also be found under the ‘Resources’ menu on Europe PMC.

As always we welcome your feedback on this new development, and would be delighted to hear from you if you want to get involved.

To stay up-to-date with Europe PMC news you can also follow us on Twitter @EuropePMC_news


Friday, 12 July 2013

Why do we need 'another' PubMed?

I have just been to the BioBricks Fondation SB6.0 conference, an international Synthetic Biology conference, this year hosted in the UK at Imperial College London. Synthetic Biology is one of the most recent scientific disciplines, and draws on the themes of nature, science and engineering 'to connect fields in new ways by improving the process of taking a new biological design from conception to execution' (from SB6.0 programme: introduction from the executive programme team).

It was a good opportunity to raise awareness of Europe PubMed Central (Europe PMC), a resource that provides free and open access to biomedical and life sciences literature, as the synthetic biology discipline also celebrates openness - the BioBricks Foundation's mission is to ensure that research is conducted in an open and ethical manner to benefit all people and the planet.

Being an international conference, the questions posed about Europe PMC differed slightly to those asked when I visit an HEI, usually in the UK. Some have asked: 'Why Europe PMC? Why does there need to be 'another' PubMed?' - imagine an indignant tone when the question is asked!

So this seemed like a good opportunity to explain, and to set the record straight that this is done in collaboration with PMC. Essentially, the long term goal is to create a network of digital archives that can share all of their respective locally deposited content with others in the network. There are three primary reasons for doing this:
  • The probablity of an archive surviving over the long term is greater if there are working copies of the archive in regular use at multiple sites around the world.
  • A producer or funder of research literature often will be more inclined to make the primary deposit of its material to a locally or regionally affiliated archive, rather than to one operated elsewhere in the world - you can find out more about the Europe PMC funders here.
  • Each site can integrate the journal articles in the archive with related material, such as national or regional practice guidelines, that has particular significance to its users.
(from http://www.ncbi.nlm.nih.gov/pmc/about/pmci/)
 
Having a number of instances of the PMC database is modelled on the idea adopted for genomic data. The International Nucleotide Sequence Database Collaboration comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three databases exchange data on a daily basis, but all three interfaces offer different functionality that benefit the molecular biology community.

Europe PMC offers many additional features that have been informed by researcher wants and requirements, for example:
  • In addition to the PMC full text, Europe PMC also enables you to search the PubMed abstracts, biological patents records and more, from a single search box.
  • Information discovery is streamlined by directly linking out to gene, protein and chemical compound databases - and this list is constantly growing.
  • The citation network provides 'cited by' information for each article, and you can now identify highly cited articles by using the citation sort tool.
Coming soon:
  • The Europe PMC External Links Service, which will enable people to publish links from articles in Europe PMC to related information or tools.
  • Incorporation of ORCIDs into Europe PMC.
Find out more about these new developments on this blog, or by following us on Twitter @EuropePMC_News

Wednesday, 3 July 2013

Monographs and book chapters must become a larger part of the open access landscape

Imagine, if you will, open access as a train, running up and down the length of the country, travelling anywhere track is laid, delivering papers, books, ideas to all and sundry. Research funders have the opportunity to man the signal boxes and set the open access movement’s direction of travel. That is what the Wellcome Trust intends with the extension of our open access policy to include scholarly monographs and book chapters, part of our on-going commitment to making the research we fund open to all in order to maximise its impact.

The Trust has been very vocal about our position towards open access, but until recently monographs hadn’t been included in our policy. As a funder of research in the medical humanities, we recognise that monographs are one of the primary research outputs within these disciplines. As we value all the research we fund equally, it seemed important for us to lay down some new track and ensure that these outputs can be accessed by all. Extending our open access policy to include them seemed an obvious step.

Immediate and open access to the research outputs which arise from our funding is a longstanding and fundamental principle of the Wellcome Trust. We accept there is a cost associated with this and fund our open access policy accordingly. The fee for existing open access options - ensuring all published material is converted to XML, and then made available in html and PDF - for books currently averages around £9,500, and we anticipate the average cost to make a book chapter open access will be £1,800. Using these figures we did some cost modelling to determine how much open access monographs and book chapters would cost when forming the extension to the policy.
We estimate that when we reach 100% compliance with the extension to the policy, which in our experience takes time, it will cost the Trust roughly £775,000 a year in “monograph-processing charges”, or 0.1% of our current research spend of approximately £650 million. This includes only Wellcome Trust-funded monographs and book chapters which fit the policy’s criteria. Our policy only covers works aimed specifically at academic research audiences, so trade books and text books, for example, aren’t included – there’s more about this in our FAQs.

To make academic titles immediately and freely accessible to readers, 0.1% of our annual research spend is a worthwhile price to pay. It is easy to find examples which illustrate this. Data from YBP Library Services show that the average price for an academic book in the life sciences is around $90, (and this includes books which could be considered to be aimed at a relatively broad audience, which tend to be cheaper than those aimed at a more specialised audience). If we divide YBP’s data by those they list as “general academic” and “advanced academic” then the average price for a life sciences book is roughly $100 and $40 respectively.

With these prices and a widespread tightening of belts, it is not surprising that print runs for academic monographs tend to be in the low to mid-hundreds. When you compare this with the number of views open access books receive the contrast is stark. For example, as Open Book Publishers report, Foundations for Moral Relativism by J. David Velleman was accessed by 1,800 readers from 46 countries in its first ten days.

Funders have a unique ability to identify which research communities are essentially cut off from the open access network, explain why open access is the most effective way to communicate the books, books chapters and journal articles that those communities produce, and provide them with the material means to achieve it. Of course, those research communities, and the publishers who serve them need to adopt it too, but given the benefits funders should be confident open access monographs can move forward in the same way as research articles have been doing. There are already signs this is happening as Frances Pinter, founder of Knowledge Unlatched (a global library consortium enabling open access books), recently became the new CEO of Manchester University Press, clearly signalling that this publisher sees open access as the future. And why not?