Friday, 23 October 2015

#OAweek 2015: Open access in numbers

For Open Access week 2015, we tweeted some number-related facts about Europe PMC, reproduced with a little additional context here.

1.  #EuropePMC has over 3,447,632 full text articles, with over 1,134,397 in the #openaccess subset http://europepmc.org/FtpSite #OAweek #OAinNumbers

As well as full text articles, Europe PMC contains all of the 25.4M PubMed abstracts, plus additional content comprising a further 5M records composed of a number of things, including biological patents. Find out more here.

2.  29% of articles published in 2014 are now available as full text or #openacess  http://europepmc.org/search?query=%28FIRST_PDATE:%5B2014-01-01+TO+2014-12-31%5D%29&page=1 #OAweek #OAinNumbers

This compares to less than 7% in 2001. In particular the open access subset (which as well as being free to read, is free of some copyright and licensing restrictions) has grown enormously: from less than 1% of articles published in 2001 to over 19% published in 2014.

3.  #EuropePMC is supported by 27 Europe-based research funders, who fund research around the world #OAweek #OAinNumbers

See who they are and find links to their open access policies here.

Shutterestock/Megainarmy
4.  54,487 – the number of grants awarded by #EuropePMC funders accessed via the Grant Lookup tool http://europepmc.org/GrantLookup/ #OAweek #OAinNumbers

That’s a lot of funding!

5.  UKPMC launched on 8 January 2007, rebranded to #EuropePMC 1 November 2012 #OAweek #OAinNumbers

When we launched it was with 8 UK-based funders. Now those initial 8 have been joined by a further 19 (more if you count those who have since merged), and include a growing number of funders from across Europe.

6.  Since we started 12,279 full text author manuscripts have been uploaded – 2,128 are in the #openaccess subset #OAweek #OAinNumbers

Europe PMC is effectively a green and gold repository in that both routes to open access are supported for full text content to get into Europe PMC. Most comes via the publisher (‘gold’) route to PMC from where it is mirrored to Europe PMC. The repositories also have their own manuscript submission systems, which enable authors to use the ‘green’ route and archive their articles directly, if the work was funded by one of our funders. Any content generated via this route is mirrored back to PMC and vice versa.

Shutterstock/iQoncept
7.  1,892,647 articles are associated with one or more ORCIDs http://europepmc.org/search?page=1&query=AUTHORID_TYPE:ORCID&sortby=Relevance #OAweek #OAinNumbers

You can use the Europe PMC author-claiming tool to link your articles to your ORCID. If you have a common name or have changed your name this is a great way to make sure your articles are easily identified as yours.

8.  20 Accession types linked in #EuropePMC http://europepmc.org/Help#databasecitations #OAweek #OAinNumbers

Accession types are text-mined so that when they appear in an article a link is created directly to the relevant data record in external databases including ArrayExpress, Ensembl, the EU Clinical Trials Register and Treefam.

9.  #EuropePMC searches abstracts & full text, & covers more content. E.g. Alzheimer 100K results Europe PMC vs 80K PubMed #OAweek #OAinNumbers

Enough said! But check out tweet 1 if you want a reminder of that content.

10. 3 ways to create or sign in to a #EuropePMC account: ORCID id, Twitter or Europe PMC-specific login #OAweek #OAinNumbers

Don’t waste time typing in the same searches each week, save your searches instead so that you can easily check what new content has been added to Europe PMC. More great features planned for user accounts coming soon!



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

Thursday, 24 September 2015

Calling all bookworms...

Europe PMC Bookshelf provides free online access to books and documents in life sciences, healthcare and medical humanities. It includes full text reports from government agencies, like the UK's National Institute for Clinical Excellence (NICE) and the US's Agency for Healthcare Research and Quality, and content allowed by participating publishers. Importantly it also includes scholarly monographs and book chapters arising from Wellcome Trust funding, which were included in its commitment to open access with an open access monographs policy created in 2013.
NextMars/Shutterstock.com
All Europe PMC Bookshelf content can be browsed hereEurope PMC Bookshelf can be searched in the same way as other Europe PMC content. A free text search on Europe PMC includes books: if a book is found on the Bookshelf, an icon will indicate the existence of a ‘Free full text book’, or you can refine your search by selecting 'Books and Documents' from the 'Popular content sets' filter on any search results page. You can additionally refine your search for a particular book if you know the publisher or editor, which can be specified via either the Advanced Search 'Bibliographic fields' menu or using search syntax as defined in the Books reference table.

Bookshelf content can also be accessed via both the SOAP and RESTful web servicesCopyright to all materials deposited in Bookshelf remains with the publisher or individual authors/editors, whichever is applicable.


Connel/Shutterstock.com
We’re excited to include books in our collection as we believe that you should be able to find the peer-reviewed information you need regardless of what format it is published in – this is an important step in that direction.


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

Friday, 17 July 2015

‘Let me count the ways.’

Title quote from ‘Sonnets from the Portuguese’, Sonnet 43, by Elizabeth Barrett Browning.

Our relationship with ORCID personal identifiers blooms in a number of ways:



ORCID Wizard
Europe PMC was an early adopter of ORCIDs allowing researchers the ability to link articles to an ORCID using our easy-to-use article claiming Wizard. Not only can this route be used to easily update your ORCID profile, article records on Europe PMC now also reflect the association, which allows...




ORCID search
You can search for authors using their ORCID, allowing unambiguous discovery of articles by Smith J (0000-0002-6143-0421), Smith J (0000-0001-6313-3298) and Smith J (0000-0001-8768-1918) – I could go on! – for example. For more on how to do this see the guidance we provide here.





ORCID login
You can use your ORCID to create/sign in to a Europe PMC account that enables you to save search queries.




ORCIDs associated with grant records
We were among the first to incorporate ORCIDs into a definitive set of grant data in our Grant Information System (GRIST). GRIST contains all of the data provided to us by the 27 Europe PMC funders – now encompassing over 52 000 records. Some of the first ORCIDs associated with grants have recently been received from the European Research Council and will be followed, among others, by those provided by the Wellcome Trust who are mandating that all applicants provide an ORCID when they apply for grants from August.

The Europe PMC Grants RESTful web service has been reconfigured to enable those using it to query records using an ORCID.

Europe PMC and ORCID in numbers


  • 2,171,651 ORCID-Europe PMC article associations.
  • 1,668,987 Europe PMC articles associated with one or more ORCIDs.
  • 125,983 unique ORCIDs associated with Europe PMC articles.
  • 21,194 people have claimed articles using the Europe PMC Wizard.
  • Over half of all ORCID-article associations can be resolved using Europe PMC, i.e. over half of claimed publications are life sciences research.
  • 25 grant records include an ORCID – watch this number grow!
  • 17% of 2013 Europe PMC articles are associated with one or more ORCID.
ORCIDs have been embraced by the research community, and we were there at the start.



Our posts have taken a floral theme lately – orchids here, irises last month.

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

All images Shutterstock.com

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 / Shutterstock.com
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’.


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


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 / Shutterstock.com

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, http://dx.doi.org/10.6084/m9.figshare.1299540). 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).


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

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: https://publons.com/author/259342/alex-bateman#profile

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: http://europepmc.org/abstract/MED/22004514), 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

Friday, 1 May 2015

The Europe PMC funders' group is expanding...

We're delighted that 2 new funders have joined Europe PMC, bringing the total to 28!
The new funders are:




Alzheimer's Society is a membership organisation, which works to improve the quality of life of people affected by dementia in England, Wales and Northern Ireland. Many of their 20,000 members have personal experience of dementia, as carers, health professionals or people with dementia themselves, and their experiences help to inform the work of the Society. They fund research into the cause, cure, care and prevention of dementia, including Alzheimer's disease, to improve treatment for people today, and search for a cure for tomorrow.






Leukaemia & Lymphoma Research is a leading UK cancer research charity dedicated to improving the lives of patients with all types of blood cancer, including leukaemia, lymphoma and myeloma. They fund research to improve patient diagnosis, develop new treatments and personalise treatments for all blood cancer patients. Through researching the cause of blood cancer, they hope to one day stop the development of it all together.

Scientists and clinicians funded by these 2 funders will join
thousands of others who make their published research articles freely available from Europe PMC as soon as possible, and in any event within six months of publication.
For more information about joining Europe PMC, visit our website:

Friday, 27 March 2015

Access to Understanding 2015: Who Won What?

With the Access to Understanding awards ceremony just about wrapping up, we can now announce the winners…

First place was awarded to Philippa Matthews for her entry ‘Rolling back malaria: A journey through space and time’, which described research exploring the changing patterns of malaria risk across Africa. The piece was praised by our judges for its enthusiasm, clear writing style, and sense of narrative; “using the facts to tell the story” with a “sense that the research team were on an expedition”. Congratulations Philippa!


Second place went to Juliet Lamb for her entry ‘Who you are, or who you’re with? Age predicts disease risk’. The judges felt that it was confidently written” and did a “great job of clarifying the use of mathematical models in research”. And third place was awarded to Peter Canning for his entry ‘Breaking through cancer’s acid shell’ which “didn’t shy away from the hard science” of drug absorption in the acidic environment around tumours.

And finally, the People’s Choice Award – a key part of our competition – read by you and voted for by you. The overwhelming response to the award, with over 1600 votes across all entries, yet again demonstrates the public appetite for accessible science writing. This year’s winner with over 400 votes was Sabrina Talukdar with her entry The persistent perils of puberty’. One reader commented that it was a “well written piece, making the original paper very accessible to lay people” which is exactly what Access to Understanding is about.

The standard of entries this year was very high, and it’s great to see the enthusiasm, talent and motivation of all the scientists who entered the competition.

You can read all of the shortlisted articles on the Access to Understanding website, with topics ranging from body clocks to tinnitus. If you want to delve deeper, every article is also accompanied with a link to the original research paper freely available from Europe PMC – the European gateway to biomedical research.

Friday, 6 March 2015

Vote now for the Access to Understanding People’s Choice Award

We are excited to announce voting has now opened for Access to Understanding’s People’s Choice Award!

The People’s Choice Award is an important part of the competition – since the entries are written for the public, we think they should be judged by the public. Click here or on the image below to read and vote for one of the 12 shortlisted entries.


You can vote for as many articles as you like, once a day. Voting will close at 1200 GMT on 27 March 2015, and the winner will be revealed at the Access to Understanding awards ceremony that evening.

Happy reading!

Monday, 9 February 2015

Health care and health policy reviews now available: Cochrane Database of Systematic Reviews

More than 300 Cochrane Systematic Reviews, funded under the 2007 and 2010 UK National Institute for Health Research (NIHR) Programme Grant programmes, are available on Europe PMC.

This has been a collaborative project between Cochrane, Wiley, and the Europe PMC team, and has enabled us to make this subset of full-text reviews available to access for free via Europe PMC with the functionality that papers in Europe PMC enjoy.

Cochrane Reviews are systematic reviews of primary research in human health care and health policy, and are used internationally to inform evidence-based health care policy and practice. Those included in Europe PMC investigate the effects of interventions for prevention, treatment and rehabilitation, or studies assessing diagnostic test accuracy.

We look forward to adding further reviews in the future as they become available.

Weighing up the evidence

To find Cochrane Reviews on Europe PMC you may use the search term:
(JOURNAL:"Cochrane Database Syst Rev") AND (EPMC_AUTH_MAN:y)
or use journals search box in the Advanced Search facility.

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

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

Thursday, 29 January 2015

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:

  • 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.

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.

Wednesday, 7 January 2015

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…