Europe PMC’s new unified search system: you can have it all!

Europe PMC provides a single search interface for 30 million abstracts (including PubMed) and over 3 million full text articles.

However, until now, the world of abstracts and the world of full-text articles, while connected in many ways, were developed quite independently from each other for various historical reasons. The practical consequence of this is that the two sources have different information associated with them: abstracts tend to have richer metadata, while full text articles of course have more content as well as other specific information such as the article’s licence and text-mined data citations associated with them. Until now, Europe PMC has treated abstracts and full-text articles distinctly, meaning that search results have been displayed as two separate results lists - one for abstracts and one for full text, and certain types of searches that cut across all content have been very difficult if not impossible to execute.

From this week, Europe PMC search now simultaneously operates across all abstracts and all full text articles, presenting the results as a single list. This has several immediate advantages. For example:

• Until now it has not been possible to sort full text articles by citation count. See here for the most highly cited Open Access articles.

• Or, see which articles with a CC-BY licence have been used to curate the Uniprot database. 

• PMIDs and PMCIDs can now be used interchangeably to retrieve the article record , and both identifiers are displayed clearly on both abstracts and full text

• It is now straightforward to see which full text articles you can freely access in Europe PMC, or see how many are Open Access, via the “Popular Content Sets” listed on each search result page. Try doing this with an ORCID search.

• Sorting by “times cited” gives a feel for the impact of those Open Access articles.

But perhaps the more open-ended implication of this development is that incorporating full text into the default search provides opportunities to bring nuggets of information from deep within articles to the surface, but accompanying this, challenges to filter out noise. As the proportion of full text articles available in Europe PMC continues to grow, it will become increasingly important to build on the basic Europe PMC sorting and filtering features such as relevance rank in order to help you find information quickly. Inventing new ways to navigate and explore the knowledge in articles becomes even more of a necessity in the context of big data, requiring a combination of improved information retrieval, linking, and content mining approaches. Europe PMC aims to provide the necessary infrastructure to harness effort from the wider research and content mining community to meet these challenges, putting open full text at the heart of these future developments.

We welcome any feedback from Europe PMC users on the new search, or any other aspect of the website, via comments to this post or via the Feedback tab at the bottom of every Europe PMC page.

Stay in touch with what's happening at Europe PMC by following us on Twitter: @EuropePMC_News

1. Europe PMC Consortium. Europe PMC: a full-text literature database for the life sciences and platform for innovation. Nucleic Acids Res. 2015 Jan;43(Database issue) D1042-8.

http://europepmc.org/abstract/MED/25378340

Access to Understanding: Statistically Speaking

Access to Understanding is getting bigger and better every year. The 2015 science-writing competition attracted over 300 entries from all over the world. But don’t take my word for it, explore the map below to see where they came from and what they were about.

Globalised Science

With 227 submissions, the lion’s share of entries were from the UK. But that’s not the whole story. The competition has a far more international flavour this year with our first entrants from Africa (Ghana and South Africa), a growth in entrants from Eastern Europe and an impressive 24 entrants from India (nearly 8% of all our entries).

Women and Science Communication

With 69.2% of all biomedical postgraduate degrees awarded to women, it’s not surprising that 70% of our entrants were female. In light of the wider gender imbalance in terms of published papers, it’s great to see that Access to Understanding fairly reflects the female contribution to the biomedical sciences.

Student Habits Die Hard

As ever, our entrants left things to the last minute with 57% submitting their entries in the last 24 hours, and 21% in the last hour. Busy times at A2U HQ!

The majority of our entrants were at PhD level (nearly 5 times as many PhD students entered as postdoctoral researchers), and generally our entrants were more likely to be in the early stages of their position (compare 75 first-year with 6 sixth-year PhD students). As we know already, having an article published by eLife is a great start to your research career.

With all the hard work done for our entrants, it’s just a matter of waiting. The winner will be announced at the Oscars of science writing – the Access to Understanding award ceremony at the British Library on 27 March 2015. In the meantime, stay tuned here and to the British Library Science Blog for competition details, shortlisted entries and more…

Innovation in Digital Publishing: blog series

Guest post from Lisa O’Sullivan, Director, Center for the History of Medicine and Public Health

By now it’s axiomatic that the digital world poses new opportunities and challenges for researchers, libraries, educational institutions, and publishers, which must be engaged with digital formats in a sustained and thoughtful way. The realities of this landscape encompass challenges to traditional models of publication and new expectations around access to both historic collections and new research literature. Open Access (OA) publishing and archiving is a central one of these challenges. 

Why is OA such a critical concern for libraries, researchers and publishers? (And why should you as a reader care?). In December 2013, we at The New York Academy of Medicine (NYAM) hosted an informal meeting around questions of OA. Participants discussed how issues of access to information have, ironically, been exacerbated by the growth of digital journals and electronic resources. Access to new research, whether in the sciences or humanities, is often prohibitively expensive for individuals and institutions. Authors struggle to make their work accessible to the broadest possible readership. Jill Cirasella at CUNY has produced an excellent summary of what’s at stake in discussions of OA.

The Wellcome Trust has been at the forefront in supporting open access to the research it funds in biomedical science and medical humanities, from its support of the open-access eLife journal and Europe PMC to ensuring that all research funded by the Trust is made freely available to users. As such, NYAM are delighted to be working with the Trust to coordinate a panel called Innovation in Digital Publishing in the Humanities at the American Historical Association Annual Meeting taking place in New York in January. The panel will be chaired by Stephen Robertson, professor and director of the Roy Rosenzweig Center for History & New Media at George Mason, whose Digital Harlem project has won multiple awards for innovation in digital history.

Our panel will examine OA from a number of perspectives. However the potentials (and associated challenges) of digital publishing go beyond OA to broader opportunities for readers, publishers, and writers in the digital world, whether relating to new ways of presenting archival material online, new ways of doing and sharing research, or new ways to engage larger audiences, and we will explore some of these as well.

We’ve asked our speakers to start the conversation early by giving their thoughts on the biggest challenge or opportunity facing digital publishing. This week, the blog series features two perspectives on Open Access and its implications, from Cecy Marden (Wellcome Trust) and Lisa Norberg (Barnard College Library). We will publish thoughts from Martin Eve (University of Lincoln and Open Library of Humanities), Kathleen Fitzpatrick (Modern Language Association), and Matthew K. Gold (New York City College of Technology and City University of New York, Graduate Center) over the next few weeks. Visit NYAM’s Innovation in Digital Publishing section to read them all as they go live.

Feel free to pose questions to the participants individually or as a group; they will respond on the blog and take your thoughts into consideration for the panel itself.

Science-writing competition now open!

Enter a prestigious, international science-writing competition aimed at PhD students and early career post-doctoral researchers.

The winner will receive an iPad and have their entry published in eLife. Read on for more…

For more information: http://EuropePMC.org/ScienceWritingCompetition
Questions: Engagement@EuropePMC.org

The competition is developed by the British Library, eLife and Europe PMC for Access to Understanding. It is supported by the Europe PMC Funders.

Access to Understanding is a collaboration promoting wider understanding of biomedical research findings.

Europe PMC Open Access Facts: a celebration of all things Open Access for #OAweek2014

Europe PMC does lots of things in the Open Access arena. For Open Access week 2014, we summarised some of them in a series of tweets over the course of the week. They are gathered together here:

2. Articles in #EuropePMC in the #openaccess set: http://europepmc.org/search?query=%28OPEN_ACCESS:y%29&page=1 … #OAfact #OAweek2014

3. Textminers: Access the full text #openaccess subset from #EuropePMC via the FTP site http://europepmc.org/FtpSite #OAfact #OAweek2014

4. #EuropePMC has 26 European funders with #openaccess policies http://europepmc.org/Funders/ #OAfact #OAweek2014

6. Details of Grants awarded by the #EuropePMC Funders are openly available for download via API: http://plus.europepmc.org/GristAPI/ #OAfact #OAweek2014

7. Charities combine to create the Charity Open Access Fund (COAF); articles published are available from #EuropePMC #OAfact #OAweek2014

8. #EuropePMC is a green and gold #openaccess repository http://EuropePMC.org #OAfact #OAweek2014

9. #openaccess is for life for all, not just for a limited period or for the lucky few #OAfact #EuropePMC #OAweek2014

10. #EuropePMC directly links articles to related data we find in the #openaccess full text #OAfact #OAweek2014

11. #EuropePMC articles and records are enriched by external links to other relevant content including PE summaries, data #OAfact #OAweek2014

12. #openaccess articles about #openaccess on #EuropePMC, e.g. http://europepmc.org/articles/PMC3226455 … | http://europepmc.org/articles/PMC3465200 … #OAfact #OAweek2014

14. Full text XML, high-res figures and supplemental data of OA articles via web services: http://europepmc.org/RestfulWebService … #OAfact #EuropePMC #OAweek2014

16. Search for articles with a clear CC-BY licence: http://europepmc.org/search?scope=fulltext&page=1&query=%28LICENSE%3A%22CC-BY%22%29 #OAfact #EuropePMC #OAweek2014

17. #EuropePMC now has #openaccess books as well as articles, patents, clinical guidelines and more #OAfact #OAweek2014

18. You saw it here first: #A2Ucomp launches again Nov – entrants write PE summaries of #openaccess #EuropePMC articles #OAfact #OAweek2014

We’d love to hear from you about how these Open Access resources are useful to you.

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

Evidence Finder: testing, testing!

Evidence Finder (EvF) provides a new way of searching Europe PMC that will help you find the most relevant articles more quickly. By surfacing “facts” based on biological concepts, EvF enhances the Europe PMC search, targeting relevant sentences from within full text articles. Over the next few weeks, we will be running an experiment on the Europe PMC website that will incorporate EvF and explore how it is used.


How EvF works on the Europe PMC website
 
When you search for a  gene, protein, disease or metabolite in Europe PMC, a panel of questions relevant to the query will appear next to the search results (left: EvF questions generated in response to a search for malaria).

Clicking on a question will elicit a search for assertions related to that question from the full text content of articles in Europe PMC. Relevant sentences from the articles will be displayed right on the search results page so you can quickly assess the relevance of search results (below:  EvF results in answer to the question “What causes malaria?).

The Experiment

EvF is developed by NaCTeM, and has been available via the Europe PMC labs site since February 2012, for a trial period (from 15th October 2014), EvF questions will appear on the full text search results page of the main Europe PMC website. The goal of this experiment is to provide the opportunity for Europe PMC users to try EvF in the context of their normal searching. After this trial period, we will analyse the use of EvF, and if it is popular and useful, this functionality could be incorporated into the Europe PMC website.

Try these examples to get started using EvF:

RAF1 | diabetes | COPD | bevacizumab | hypertension

“Evidence Finder pushes the limits of searching the scientific literature," says Jo McEntyre, head of Literature Services at EMBL-EBI. "There is so much information buried deep within research articles;  we have to constantly invent better ways to capture and capitalise on these insights. Now, in the era of big data and open science, we can be more innovative than ever before."

Feedback

We are very interested in any feedback you would like to give us on your experiences using Evidence Finder, and would love to hear from you: please use the blue Feedback tab at the bottom of every Europe PMC page, post a comment on this blog entry, or email us at helpdesk@europepmc.org.

Furthermore, if you are a text or data miner who has developed an algorithm or application that adds value to the full text open access content, and would like to explore how to link up with Europe PMC, we would like to hear from you.

Further information about EvF can be found in the FAQ:

http://labs.europepmc.org/docs/EvidenceFinder.pdf

Stay in touch with what's happening at Europe PMC by following us on Twitter: @EuropePMC_News

Linking grants to your publication

It is important that you add all appropriate grant information to relevant papers on Europe PMC to support:

• Grant Reporting
• Compliance with Funder open access policies
• Data Consistency    
• Resource Discovery
• Author Claiming

There are a variety of routes that enable grants to be linked to papers in Europe PMC.  We have outlined these below to enable authors and Funders to choose the most appropriate route(s) to ensure that the grants used to support their research are correctly attributed:

1. Using the Europe PMC plus Grant Linking module

This option is only available to PIs (Principal Investigators) of grants from the Europe PMC Funders. Log in to Europe PMC plus and select the Grant Linking tab to associate papers with your grants.

Note: Linking grants to PubMed papers does not signify compliance to your Funder’s mandate. Full text versions must either be deposited directly by the Publisher or self-archived. See http://europepmc.org/FAQs#respubs for more information.

2. When self-archiving author manuscripts via Europe PMC plus

All appropriate associations can be made as part of the submission process of Europe PMC Funder grantholder research articles.

3. Bulk grant linking

This option is open to members of the Europe PMC Funders group, who can submit a list of articles (identified by PubMed ID) and grant IDs. We will then create the appropriate grant-article associations, which will display in both Europe PMC and PubMed.

4. When the paper is indexed by NLM indexers

This option only applies where the research has been supported by one of the original eight funders of Europe PMC. Grants will automatically be added to PubMed papers during the indexing process if the grant has been correctly acknowledged in the paper.

5. Direct pipelines

Grant-article associations are collated from various sources, including Researchfish; all associations are applied to Europe PMC and validated ones pushed through to PubMed.

You can search Europe PMC using a grant ID to find all papers associated with a particular grant number, using either the advanced search form, or the the following search syntax:

Europe PMC also has a Grant Lookup Tool which holds detailed, consolidated grant information across all Funders. The data is also available via an API.

This post is by Rob Rowbotham, Europe PMC Helpdesk Manager.

For more information, please contact the Europe PMC Helpdesk at:

helpdesk@EuropePMC.org

Stay in touch with what's happening at Europe PMC by following us on Twitter: @EuropePMC_News