Tuesday, 2 December 2014

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.

Tuesday, 11 November 2014

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.

Friday, 24 October 2014

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: #OAfact #OAweek2014

3. Textminers: Access the full text #openaccess subset from #EuropePMC via the FTP site #OAfact #OAweek2014


4. #EuropePMC has 26 European funders with #openaccess policies #OAfact #OAweek2014













6. Details of Grants awarded by the #EuropePMC Funders are openly available for download via API: #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 #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. | #OAfact #OAweek2014













14. Full text XML, high-res figures and supplemental data of OA articles via web services: #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

Friday, 17 October 2014

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?).

screenshot.png

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:


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

Friday, 26 September 2014

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

Wednesday, 20 August 2014

Using Europe PMC’s export options as research funder

Recently Europe PMC released new export format options, to help users get Europe PMC’s wealth of metadata (and our open access papers) into the file formats they like to use.


We’ve already posted about how useful this function is for researchers, but it’s great for research funders too. Funders can convert their carefully constructed search into a tab separated file and use Excel to manipulate the metadata as they wish.



Funders can find out how many papers acknowledging their funding have been made open access, what research areas papers are being published in, or which grants papers are linked to, among other things!