Wednesday, 24 June 2015

IRIS, educated – more accurately, populated…

“Education doesn't make you happy. And what is freedom? We don't become happy just because we are free, if we are. Or because we have been educated, if we have. But because education may be the means by which we realize we are happy. It opens our eyes, our ears. Tells use where delights are lurking. Convinces us that there is only one freedom of any importance whatsoever: that of the mind. And give us the assurance, the confidence, to walk the path our mind, our educated mind, offers.”
(Iris Murdoch)

Added in September 2014, Europe PMC’s RESTful Web Service has a Dublin Core response, complementing existing XML and JSONformats. The new response is compliant with the Dublin Core Metadata Initiative (DCMI), which supports shared innovation in metadata design and best practices across a broad range of purposes and business models. For many organisations this format is the most acceptable way to exchange article metadata, and for this reason we wanted to implement the response in our service.

Earlier this year the World Health Organization (WHO), a Europe PMC funder, made use of the service’s Dublin Core format to populate their DSpace Institutional Repository for Information Sharing (IRIS – hence the only slightly tangential quote by Iris Murdoch!).

In case you haven't already had enough of spurious references to Irises...
Elena Larina /
IRIS provides free access to public health-related knowledge. This includes information produced directly by WHO, as well as WHO-authored articles that have been published in peer-reviewed scientific journals – the latter collection is provided to IRIS via Europe PMC’s RESTful Web Service, and now numbers in the region of 1800 records comprising metadata  and open access PDF full text files, on topics ranging from ‘Effect of high-dose or split-dose artesunate on parasite clearance in artemisinin-resistant falciparum malaria’ to ‘Distribution of yellow fever vectors in Northwestern and Western Provinces, Zambia’.

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Wednesday, 17 June 2015

Wiki’d!: Links from Europe PMC articles to Wikipedia

Europe PMC has a new provider of External Links: links from articles on Europe PMC to related content on 3rd party websites. Our most recent addition provides links from over 300,000 articles to entries in Wikipedia: the free encyclopaedia. For example, from the article ‘Spinal subdural abscess following epidural steroid injection’, you can link (via the External Links tab) to a Wikipedia entry about abscesses – though I don’t recommend trying this one if you’re at all squeamish! How about ‘ponesimod’? – it sounds like it could be some sort of insect, but is actually an experimental drug for the treatment of multiple sclerosis and psoriasis (linked from Europe PMC article ‘Mass balance, pharmacokinetics and metabolism of the selective S1P1 receptor modulator ponesimod in humans’).  You can find out more about Ebola virus disease via for example, ‘Ebola virus disease: an update for anesthesiologists and intensivists’. Actually ‘intensivist’* is the term that I hadn’t heard of in this instance – we should all be more aware of Ebola after the recent outbreak in West Africa.

Evan Lorne /

The terms linked to are many and varied. Research articles often assume a certain amount of knowledge on the part of the reader. The addition of links to Wikipedia entries provides further explanation of some terms that might not be explained in ‘lay’ terms in a research article. Europe PMC also supports lay explanation of research through the Access to Understanding science-writing competition where entrants produce plain-English summaries of selected research articles available from Europe PMC.

The technical bit
Several Wikipedia entries cite peer-reviewed research articles. Wikimedia has recently released a dataset of scholarly citations in the English Wikipedia, which are identified by PubMed or PMC ID (Halfaker, A., Taraborelli, D. (2015) Scholarly article citations in Wikipedia, Figshare, The dataset currently includes the first known occurrence of a PMID or PMCID citation in an English Wikipedia article and the associated revision metadata. We have used our External Links resource to publish links from articles in Europe PMC to those entries in Wikipedia that contain a PMID or PMCID citation.

The process for providing us with links is really straightforward and we provide step-by-step instructions and support – you don’t need to be a web developer to do this.

Help people discover your information. If you have some content that would enhance the articles in Europe PMC, then have a go!

*Intensivist: A physician who specializes in the care of critically ill patients, usually in an intensive care unit (ICU).

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Wednesday, 10 June 2015

A step towards open peer review

Peer review is the cornerstone of how we decide what research to publish. As currently implemented, it generally consists of two or three referees giving anonymous comments on a research article prior to publication ... or ... rejection. Much has been written about the failings of this process (a very small sample of illustrative references are given below). A few brave new journals are exploring new models of peer review, driving more openness, notable examples being the BMJ and F1000 Research, while software and standards that enable comments on web pages make post-publication peer review technically possible. Why then, given decades of both grumbling and discussion, do we still cling to a process that was invented for a different technological era? Open and post publication peer review represents a sea change in behaviour across a community: we are a conservative lot and this will not happen fast, which is probably for the good as not everything about peer review is wrong.
One of the issues at the heart of the matter is that peer review is something that every researcher spends time doing, for which they receive no credit, in spite of the generally agreed opinion that it is a Good Thing. The lack of credit is exacerbated by the culture of anonymity that surrounds peer review - how can you be credited publicly for something that can only be seen by a handful of people?
Image Shutterstock 284306789
Enter Publons: a start-up that aims to help researchers get credit for peer review (ref. Wikipedia). They have quite nimbly navigated the complexities of anonymity and credit by putting you, the user, in control of how much to reveal of yourself as a reviewer. By sending Publons the acknowledgement email received on completion of a review, Publons adds a note that you have reviewed for that journal in a given year - which suits classic-style anonymous reviews. If you wish, you can upload the review you wrote, make it public (unless the journal forbids it), and link it to your profile. Publons assigns points for each review, so the more reviews you register, and the more open you get, the higher your score. As yet, the review stubs are not pushed to ORCID, although you can use ORCID to log in and display your ORCID iD on your Publons profile page. See Alex Bateman's profile as a nice example:

Via the Europe PMC External Links Service*, there are now almost 40,000 links from articles in Europe PMC to reviews on Publons. While open pre-publication reviews are still only available in a minority of cases (see for example:, the framework is nevertheless there to build on this more open behaviour. We except the number of available reviews to grow as Publons partners with publishers, reviewers get bolder, and post-publication options are used.

Just one grumble (there had to be one somewhere): browsing the reviewers on the Publons website, the gender balance, or lack of it, is striking. I counted only ~6 women in the top 100 reviewers. Whether this is an artefact of the early adopters of Publons or indicative of deeper bias in the peer review system, more openness can only inform.

*The Europe PMC External Links Service was launched in 2013 and is a mechanism for people to publish links from articles in Europe PMC to related information or tools. The service has enabled articles on Europe PMC to be enriched with links to content as varied as data, press releases, and article full text (where it’s not already held by Europe PMC).
All of our External Links providers can be discovered by using our advanced search page – the field at the bottom of the form. You can find out more about the Europe PMC External Links Service and how to get involved here.
Contributed by Jo McEntyre (@jomcentyre) and Anna Kinsey.

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