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: #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?).


The Experiment

EvF is developed by NaCTeM, and has been available via the Europe PMC labs site since February 2012, for a six-week period (from 15th October 2014 to 26th November 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."


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

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 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:

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!

Wednesday, 6 August 2014

New export options now available: use Europe PMC to populate your bibliographic references in EndNote, Reference Manager etc.

Europe PMC has released new export format options, indicated in the image below:

The RIS export format is typically used by Reference Manager and EndNote bibliographic applications for example, so you can now easily import Europe PMC citations.

You can also email citations to yourself, or others, by selecting this destination option from the Export menu and filling in the required address fields.

Identifying articles and populating your reference list now just got easier using Europe PMC.

More information can be found here:

Stay up-to-date with Europe PMC news by following us on Twitter, @EuropePMC_News

Friday, 18 July 2014

Taylor & Francis Open Access Survey: translating values into licences

Guest post from Alex Green, Transformation Project Co-ordinator, Wellcome Trust

Last month saw the publication of the 2014 Taylor & Francis Open Access Survey. Combining responses from just over 7,900 authors who published with Taylor & Francis in 2012 (9% of the total), this represents the opinions of authors from across the world in roughly the proportions they have published with Taylor & Francis – although my inner data geek really wants to get hold of the full dataset to apply some weighting to the under-represented authors of East and South East Asia.

The Taylor & Francis survey shows strong support for open access (OA) publishing by authors and a clear belief in its benefits compared with traditional publication, which has increased from the 2013 survey. 70% of respondents also disagreed or strongly disagreed with the statement ‘There are no fundamental benefits to open access publication’, up 10% from 2013.

However, when read alongside this evidence of increasing widespread positive attitudes to OA publishing, the findings on licensing are striking. In particular, the preference for more restrictive licenses seems at odds with the attitudes and values expressed by authors in response to the Section 1 questions on that topic. For example, in Question 5, 71% of authors were happy for their work to be re-used without prior knowledge or permission for non-commercial gain provided they receive attribution. This is equivalent to a CC-BY-NC licence, but only 18% of authors selected this licence as their first or second choice when answering Question 6 (see graphic below).

Question 5

Question 6

This mismatch between author attitudes and licence preference seems common to nearly all responses. Again in Question 5 authors seem concerned about commercial reuse of their work without prior knowledge, with 65% disagreeing that it is acceptable. However in Question 6, 47% selected Copyright Assignment as their first or second preference for licensing making it the second most popular licence along with Exclusive License to Publish. Having assigned copyright away, authors would have little control over any commercial reuse, not least by the publisher they have assigned the copyright to.

There are several hypotheses we could explore to account for this seeming contradiction. Looking down the results for Question 6 there is a clear drop off towards the bottom of the list for ‘preferred licences’. It would be interesting to know if these options were always presented in the survey in the same order that they are presented in the report. If so, we may be seeing response order effects (Krosnick and Alwyn 1987), but unfortunately full details of the methodology are not openly available along with the report. 

The contradictions between responses may also be partly due to a degree of satisficing, an effect where respondents choose adequate answers rather than optimal answers because it is easier to pick the first acceptable, or most familiar, option than fully evaluate all options (Simon 1957, Krosnick 1991). This could be leading to selection of the more familiar Copyright Assignment and Exclusive License to Publish over the various Creative Commons licence combinations.

Finally, it’s probably relevant to note that the definition boxes provided to respondents at the start of the survey gave explanations of different modes of OA publishing, repositories and text- and data-mining but not the differences between the licences. These aren’t always easy to grasp, especially when completing a survey at speed – I don’t mind admitting that I had to check with a colleague on the exact differences between the various licence options. Perhaps, as Dr David Green, Global Journals Publishing Director said in the Taylor & Francis press release, there is still ‘much work left to do in simplifying our policies and documentation so that our author communities are in no doubt as to what their OA options are’.