Monday, 18 April 2016

Europe PMC, Wikipedia and Wikidata - opportunities for deeper integration

Since our blog post last summer on the inclusion of Wikipedia as an external links provider, we have been lucky to host an intern, Tom Arrow,  who has spent the last few months investigating possible further connections between Wikimedia projects and Europe PMC. This post highlights some of the ways Tom has been exploring these connections.


When have PMC/Europe PMC articles been added to Wikipedia?

Using an updated version of the same dataset that created the external links (as mentioned in our blog post in June) produced by A Halfak and D Taraborelli (doi:10.6084/m9.figshare.1299540) Tom made a plot of the number of citations in English Wikipedia to articles in the PMC dataset against time. 
This is available at: https://plot.ly/~tarrow/32/first-appearance-of-pmcids-on-wikipedia. Here you can observe the continued increase in PMC citations on wikipedia. The steep points are times when automated processes added PMCIDs to citations that previous only had DOIs.


Uploading article metadata to Wikidata

Wikidata is a Wikimedia project to store structured data for inclusion in both projects like Wikipedia and the world at large (doi:10.1145/2629489). Tom has been investigating ways to share metadata from Europe PMC with this project to increase public exposure to, and interaction with, the metadata. Initially we have focussed on metadata for Europe PMC Open Access articles that are cited in Wikipedia. From a total of around 70K articles metadata was created for 15K.

He has been creating items about journals, journal articles and authors on a server running the same software as Wikidata, Wikibase. All of these items are being created using data consumed from the Europe PMC RESTful web services. While this work is still in progress the results can be seen at Librarybase.

This was done by the production of various Python scripts which are available on GitHub. First, a Python client for the Europe PMC RESTful webservices API, available here https://github.com/tarrow/epmclib, was created. This enables use of both core and lite API queries for functions such as getting the title of an article, checking if a PMID or PMCID resolves, and getting a dictionary of basic metadata about and article. This client could easily be reused by other consumers of the API.

A second package of scripts is available at https://github.com/tarrow/librarybase-pwb, which uses and extends the popular pywikibot suite for interfacing with MediaWiki and Wikibase sites. These scripts form a foundation for making and curating Wikibase items relating to bibliographic metadata from Europe PMC.

Finally, two utilities for discovering which citations appear on which Wikipedia article were written; both rely on the mwcites utility written by Aaron Halfak. One is for processing the output of mwcites in bulk for importing thousands of articles at a time into Librarybase (https://github.com/tarrow/queryCitefile) and the other produces a realtime stream of citations (https://github.com/tarrow/citationslivefeed) as they are added or removed from Wikipedia which can be used to keep Librarybase up to date.

This work demonstrates how the Europe PMC API can be used to share Europe PMC more widely, lowering the entry barrier to its use with a basic Python client, and provides a next step to link Europe PMC and the Wikimedia communities. It enables straightforward analysis of academic citations in Wikipedia, and may help people find more useful papers.

Monday, 11 January 2016

Open Author Profiles at Europe PMC: ORCIDs in Action

We are excited to announce the launch of the Europe PMC author profile pages! Based on your ORCID record, they provide a graphical overview of your publications in Europe PMC and your citation rate over time.

With over 2.2 million articles in Europe PMC linked to about 172,000 unique ORCIDs, we expect this feature to be of wide interest to publishing researchers, journals, funders, and others interested in scientific credit.

Author profiles tour

All you have to do to see your profiles is add your ORCID to the URL:

http://europepmc.org/authors/0000-0000-0000-0000 where 0000-0000-0000-0000 is your ORCID. Alex Batemans looks like this:



At a glance you can see how many of your publications are freely available as full text in Europe PMC (blue) and a count of your open citation (line plot), per year.

Each article making up the profile is also listed individually, together with a graph showing citation over time of each article. It’s interesting to see the different profiles of articles:

1. Some have had their day:Screen Shot 2016-01-11 at 11.34.23.png
2. Some are abidingly cited:Screen Shot 2016-01-11 at 11.35.28.png
3. Some are a slow burn:Screen Shot 2016-01-11 at 11.36.33.png

How do I get an author profile page?

Europe PMC profile pages are based on publically available data. If you have an ORCID, and you have listed your life sciences articles in it using the default (public) settings, then you will have a Europe PMC profile page.

An ORCID is a unique identifier that distinguishes you from other researchers. If you don’t have an ORCID, it takes only a couple of minutes to get one from the ORCID foundation. Then linking articles to your ORCID only takes a few minutes using our ORCID claiming tool.

How do I access my own, or another author's profile page?

As well as via direct links such as http://www.europepmc.org/authors/0000-0001-8314-8497 , there are various other ways access an author’s profile including:
  1. From a Europe PMC abstract page. Under the abstract, authors that have ORCIDs linked to the article are listed. Click on the author’s name to see the profile of that author. Screenshot 2016-01-11 10.20.41.png
  2. Search for an ORCID. If you know a person’s ORCID, just type it in the search box on any Europe PMC page. At the top of the results list there will be a box displaying the name of the person and a link to their profile.Screen Shot 2016-01-11 at 12.33.08.pngScreen Shot 2016-01-11 at 12.35.25.png
  3. Advanced Search. If you know the person’s name, but not the ORCID, use the author search feature in the Advanced Search page. If there is an ORCID for that person in Europe PMC, it will be shown in the autosuggest list, along with an affiliation to help you disambiguate further:Screen Shot 2016-01-11 at 12.39.18.png

Author profiles are on trend ...

The announcement last week that several leading publishers will require ORCIDs in publications from 2016 onwards will have a direct effect on adoption, as well as encouraging other publishers to take the same position in the longer term. Coupled with the recent launch of CrossRef’s ORCID auto-update feature, in which published articles are pushed to ORCID records on the authors’ behalf, ORCIDs are increasingly becoming embedded in publication workflows. Several funders, including four that use Europe PMC as a designated archive for the research they fund, now either require (Wellcome, NIHR, FWF) or request (ERC) ORCIDs in grant applications. Looking further to the future, the European Commission’s recently funded THOR project is exploring how public datasets can be linked to ORCIDs.

Given these positive trends, we hope the Europe PMC author profiles not only prove of interest and use to researchers but also contribute another facet of clarity for open science. There’s no time like the present to update your ORCID record and see what it looks like through the lens of Europe PMC author profiles!
Useful links
ORCID foundation


Contact us at: engagement@europepmc.org or on Twitter @EuropePMC_news

Thursday, 7 January 2016

New Year, New Look for Europe PMC

You may notice that the Europe PMC website looks a little different. Perhaps a little clearer, neater, bolder? More importantly, we also hope that it is easier to use and to find key information about Europe PMC. Yes: we have given the Europe PMC website a makeover to celebrate the New Year!

In particular, we have redesigned the homepage and navigation, and the website is now responsive for use on mobile devices. Over the past few months we have carried out a programme of user research and gathered lots of feedback to improve the site.

Key new features on the Europe PMC website


(1)  Mobile phone and tablet friendly - Europe PMC pages now scale according to the size of your screen automatically.

Before redesign
After redesign
Screenshot_2016-01-06-11-57-20.jpg
Screenshot_2016-01-06-11-57-42.jpg


(2)  Navigation - the main menu items have been simplified and reorganized to help people find information on Europe PMC, tools, and data more easily. We have added info-graphics to help explain the scope of content and main offerings. The navigation is also repeated in full at the bottom of every page.

(3)  Consistency - we have changed the fonts, spacing and link styles to be more consistent and improve on-screen readability.

(4) Accessibility - in addition to being responsive, the site is now much more accessible for people using assistive technologies.

In 2014 we conducted in-depth usability studies on the website, involving 15 people with life sciences research, clinical and information science backgrounds. From this work we were able to identify a number of areas in which the website could be improved. One of these – providing a unified search with a single list of search results – was addressed last year, but our new design has taken more time to mature. We have sought further help from our users along the way during the design process.

We created several design concepts and gathered feedback from over 60 people using an online usability testing tool. We then carried out further usability studies as the website design progressed.

Thanks to everyone who provided time and input into the design of the new site. Hopefully you will be able to spot the implementation of some of your opinions in our new design.


We welcome your feedback and opinions on how it looks and works for you. We will be making further improvements in 2016. Contact us at: engagement@europepmc.org or on Twitter @EuropePMC_news

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