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Updates from Europe PMC, a global database of life sciences literature

Europe PMC team

 | 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!


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Partnerships & funding

Europe PMC is a service of the Europe PMC Funders' Group, in partnership with EMBL’s European Bioinformatics Institute (EMBL-EBI); and in cooperation with the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NCBI/NLM) . It includes content provided to the PubMed Central (NLM/PMC) archive by participating publishers.