Tuesday, 20 December 2016

Europe PMC - a year in review

This has been a very busy and fruitful year for Europe PMC. With holidays approaching we take a look back at some of the Europe PMC achievements and milestones of 2016.
We kicked off in January with a new, mobile-friendly homepage and information pages. The final design was based on user research in which we gathered lots of feedback from you to come up with design concepts, which were thoroughly tested again before release. We still have work to do on improving these pages and we intend to chip away with making them better, based on feedback, throughout 2017.
Our spring was focussed on the migration of manuscript submission services from JISC to the EMBL-EBI. We installed a database (developed by JISC) that contains information on all the grants awarded by the funders of Europe PMC. This information is important to us to authorize the upload of manuscripts from grant holders, but we also make the data discoverable on the Europe PMC website via the grant finder, or programmatically via the GRIST API. Over 2500 grants have been added by our funders since the spring and the database now includes more than 56,000 grants, crosslinked to the articles they supported.
Summer was a hot time for us. One of the key objectives for Europe PMC is to enable application developers and text miners to reuse the open access full text content, in order to find innovative approaches to searching, filtering and reading the scientific literature. Towards this goal, in July we launched SciLite - a tool that allows text-mined terms to be displayed as an overlay on research articles. For Europe PMC users, SciLite makes it easier to scan articles for key concepts and provides deep links with related data. For text miners, it is an opportunity to showcase their work to a wider public. SciLite is based on the Web Annotation Data Model and is open to any text-mining group. So far, SciLite operates on articles with a CC-0, CC-BY or CC-BY-NC licence, and has contributions from the National Centre for Text Mining (NaCTeM) and the Bibliomics and Text Mining group at the University of Applied Sciences, Geneva, as well as from the core Europe PMC text-mining pipeline; the number of contributors is set to grow in 2017. All the full text annotations are available via a SPARQL API.
As a part of our mission to deliver a world-class service for all of our users, we took a major step towards improving our search by migrating Europe PMC indexing to Solr in the late summer. This has already significantly improved the speed with which we can return search results, as well as making our indexing of new content more efficient. As well as these basics, Solr comes with some useful features built-in, such as filters, auto-suggestions, and snippets, which we plan to start exploiting next year. Other search improvements introduced in 2016 include the addition of reverse sort orders for “date” and “times cited”, so that you can see results ranked by “oldest first” or “least cited”, and the ability to search by embargo date (as well as their display on abstract pages).
Finally, for the summer, our family of 27 funders was joined by the Academy of Medical Sciences (AMS), who became a member of Europe PMC so that the research they fund can be archived in Europe PMC, supporting their open access policies.
We are always open to new opportunities to improve on existing services. This year our External Link providers, who link out from the content in Europe PMC to their resources, can now display an image alongside the link itself. Already the iconic Altmetric donut is apparent on articles under the “External Links” tab, the CitePeer icon alerts users to alternative reference lists on the Related Articles tab, and the ImpactStory badge can be seen on the Author Profile pages. The Author Profile pages are generated for every researcher with a paper in Europe PMC listed in their ORCID profile, and their number has been constantly growing throughout the year. Currently, there are about 350,000 life science researchers actively publishing and using their ORCIDs, having claimed about 3.5 million articles available in Europe PMC.
Our autumn has been about building a program of community engagement and starting research projects with users that will inform next year’s development. The Europe PMC team has now expanded to include a community manager. We hope that this will help us to connect and reach out to all of our stakeholders, create opportunities for networking and discussions, as well as to identify useful synergies. It’s critical to us to understand the needs of our user community and their goals, and manage Europe PMC services accordingly. Finally, as part of our community engagement, we aspire to be open about our development plans in order to gain feedback at the earliest opportunity. So we have concluded this year with the publication of a roadmap that summarizes our recent accomplishments and highlights our near-term development plans, which we will update quarterly on the Europe PMC website. As always, we welcome your feedback. Leave a comment, send us an e-mail, or connect with us via Twitter.
We are looking forward to 2017 and wish all our users happy holidays. Season’s greetings from Europe PMC!

Monday, 7 November 2016

Growing connections: new Community Manager at Europe PMC

What exactly is Europe PMC? How is it different from PubMed Central? What can I do with Europe PMC?
Those are some of the questions I had myself when I first heard of Europe PMC. And now my task is to make sure that everyone can answer them easily.
My name is Maria Levchenko and I am a recent addition to the Europe PMC team. As a Community Manager I am responsible for reaching out to all of our users, informing them about new developments, but also gathering their valuable feedback, in order to make our services even more user-friendly and helpful for everyone.
My background is in biomedical research. I have also briefly worked at the European Research Council – one of the science funders that support Europe PMC – to better understand how funding agencies shape the way we do science.
My interest in Europe PMC stemmed from their goal to create a world-class literature resource. I am passionate about tools that help the scientific community on their quest for knowledge, and I believe that Europe PMC can do for research what Google does for our everyday life.
Our mission is to build open, full-text scientific literature resources and support innovation by engaging users, enabling contributors and integrating related research data. Europe PMC provides access and adds value to more than 30 million abstracts and almost 4 million full-text articles. All of the content in Europe PMC is free to read and we strongly support open access, in order to make the scientific literature available to everyone. On top of the core content, we see Europe PMC as a community-sourced platform for new developments that will improve the ways we can search, browse and integrate the literature with research data. We strive to be open about our work so that anyone can use the services and create new tools. We want to foster a sense of collaborative community, and this is where I come into play. My role is to connect with you, our users, provide you with the means to read and use the content and make your own contributions, helping to make Europe PMC a useful resource for scientists, developers and the general public alike.
In the coming weeks and months, I will be sharing news about our work, providing useful materials on how to use our service, as well as responding to your feedback.
We invite you to tell us what you think about Europe PMC and its role in your professional life. Leave a comment, send us an e-mail at helpdesk@europepmc.org, or connect with us via Twitter @EuropePMC_news.
Looking forward to hearing from you!

Friday, 9 September 2016

SciLite Annotations

Manual curation is vital for maintaining quality information in biological databases. However, with the exponential growth in biological data this approach is both challenging and time consuming. We wanted to create a scalable and sustainable process which could complement manual curation.   

We recently launched a new service - SciLite - that allows text-mined annotations to be displayed on research articles. The aim of this effort is to promote sustainability of curated databases by bridging the gap between literature and data. To this end, SciLite:
  • supports database curation processes, by highlighting biological concepts, making it easier to find key concepts described in articles;
  • provides a mechanism to link those concepts to the related resources, for efficient data integration. 
SciLite's open design enables community-driven annotations, from text-mining groups, and manual annotations, to be made available to Europe PMC users.

What are SciLite annotations?

SciLite annotations enable biological terms and concepts, such as genes/proteins, diseases, organisms and accession numbers, to be highlighted on full text articles in Europe PMC. Using the check-boxes on the right-hand side of article pages, readers can select the types of concepts that they are most interested in and matching annotations for that article will be highlighted on the article text as below. 







Clicking on the highlighted terms in the text opens a popup with a link to related database record. In the example below, an interactive Protein Data Bank (PDB) structure model is also provided when you click on a highlighted PDB accession number.


When annotations are provided by the text-mining community, the source of the annotation is displayed. In the example below, the Gene Reference into Function (GeneRIF) annotations were provided by the Text Mining group at HES-SO, Geneva, Switzerland.


Another text-mining group - NaCTeM - has provided phosphorylation event annotations, as shown below.



Take a look at this example article with annotations.
Annotations are displayed on articles with a CC-BY, CC-BY-NC or CC-0 license.

How are annotations generated?

The biological terms and concepts are identified by text mining algorithms, which are developed by a variety of text mining groups. Any text-mining group can participate in this scheme. Once concepts of interest have been identified within the text, they are formatted according to the W3C Web Annotation Data Model, and stored in a triple store via the EMBL-EBI RDF Platform. If you are a text miner, find out how to provide annotations to Europe PMC at our SciLite annotations page.

We're improving annotations with your help

Because annotations are generated automatically by text mining algorithms, we want to ensure that annotations are useful to users of Europe PMC. On each annotation there is the opportunity to provide feedback by either marking the annotation as incorrect, or endorsing useful annotations.
Screenshot showing feedback feature for an annotation
This information is fed back to the Europe PMC team and will be acted upon, helping to improve the annotations overall.


Thursday, 4 August 2016

Academy of Medical Sciences joins Europe PMC

We're delighted to announce that the Academy of Medical Sciences has joined Europe PMC as a new funder, bringing the total funders to 27.

The Academy of Medical Sciences represents the diverse spectrum of medical science – from basic research through clinical application to healthcare delivery. Their mission is to promote medical science and its translation into benefits for society.

Scientists and clinicians funded by the Academy of Medical Sciences 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:
http://europepmc.org/Joining

Tuesday, 2 August 2016

Search improvements


"Any sufficiently advanced technology is indistinguishable from magic."
- Arthur C. Clarke

Sometimes the changes we release on Europe PMC are not immediately obvious! For the last few months we've been working hard to migrate our search to a technology called Solr. Our search has been using a Lucene-based index and customised query handler for several years. It was starting to feel the strain of the increasing number of search queries on Europe PMC (we have over 1 million unique users per month), and was proving cumbersome to maintain.

Our new search using Solr may not be "magic", but it's faster, nimbler and easier to maintain. You might notice some subtle improvements including:

Increased performance

Based on our current testing, searches are on average 20 times quicker using Solr than using the previous search engine. We will continue to test and monitor the performance of Solr.

In the graph below Solr is represented by the red line and our previous search engine is represented by the blue line. You can see over a trial period that http:// requests were processed by Solr more quickly than requests to the previous search engine.

Graph showing duration of http:// requests, comparing Solr search with our previous search


Improved title searching

If you search for part, or all, of an article title using a free text search, articles which have matching titles will appear high up in your search results. It should therefore be much quicker and easier to find articles by title.

Popular content sets are quicker to load

In the past you may have noticed that the popular content set filters (which allow you to filter results by full text articles, open access, reviews, patents, books and documents) are slow to load on our search results page. With the Solr search the filters load much more quickly.

Author profiles are updated more quickly

If you have claimed articles to your ORCID record, your Europe PMC author profile will be updated more quickly than previously. Claimed articles should appear in your profile within 30 minutes, rather than within 24 hours.


The Solr search provides a strong architectural foundation for Europe PMC, which will make it easier and quicker to introduce new search features. We will announce any future developments on this blog.

If you have saved searches you may notice that the number of new results for your search seems different. That's because Solr has a different way of handling synonyms, so it is possible that you will have more, or less, articles for your search term than the previous search

If you have any feedback about the new search, please let us know using the feedback link at the bottom of the website, or by emailing helpdesk@europepmc.org.


Thursday, 9 June 2016

5 ways to use the new Grant Finder

We've recently launched a re-designed Grant Finder on Europe PMC. You can use the Grant Finder to search over 56,700 biomedical research grants, awarded to the 23,000 Principal Investigators supported by the 26 Europe PMC funders.

Learn 5 ways to use the new Grant Finder:

1. Find a collaborator

As a researcher, or student, you can find potential collaborators / PIs working in a related research area. Search for a research topic, by entering a term in the 'Keyword' field as shown in Figure 1 below. This will search the grant titles and abstracts.

Figure 1: The new Grant Finder search

2. Find funded projects in your field

If you're writing a grant application, you can use the Grant Finder to search for grants by funder, to discover which grants a funder has recently awarded, in a similar area. If you know the name of the funding stream you are applying to, enter this in the 'Keyword' field. If you know the name of a Principal Investigator in your field, or their ORCID, you can enter these details in the relevant fields.

3. Find potential funders

As a PI you can discover which smaller funders have funded research in your area. Use the 'Keyword' field to enter in a phrase describing your research area, for example a disease or protein name.

4. Find out which publications are associated with a grant

To find out what research articles have been published, you can easily link to publications associated with a grant from the search results page (or from a grant page), as shown highlighted in red below in Figure 2 and Figure 3:

Figure 2: Links to publications appear under search results as above.

Figure 3: Links to publications on a grant page

5. Find out more about the funding from a specific article

If you are searching for articles on Europe PMC, you can see which funders have supported the research, just below the abstract as shown below in Figure 4. From here you can link to the grant page to find out more details about the grant award.

Figure 4: Funding details are shown under the article abstract.

If you are interested in using our open grant data in your website or application, find out more about how to use our GRIST API.

Let us know what you think of the new Grant Finder!





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