News blog

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

Europe PMC team

 | 21 December 2017


Looking back, looking forward: a year in review

As 2017 concludes, we reflect on Europe PMC’s landmark achievements. Let’s take a closer look at the highlights of this year.

Cutting-edge search and viewing mechanisms

Search results now display snippets – fragments of the publication text that contain matches to your query. Snippets highlight the search term in its context, making it easier to identify the relevant content you were looking for. The snippet link on the article abstract allows you to navigate directly to where your  search terms appear in the full text. Another new feature is the publication year filter, so that you can limit your search results to a particular year, or even a year range.

In addition to these search improvements we have focused on the abstract and full text display. We have added a citation graph to the publication pages, showing how frequently the article was referenced over time. The graph is a visual representation of the “cited by” information available via the Citations tab. The redesigned affiliation view helps you navigate through the list of authors, highlighting those that belong to the same institution.

User services

Last year we introduced Author Profile pages based on publicly available ORCID data. This year we have made them more discoverable thanks to the “Suggested Authors” feature. An author search in Europe PMC now brings up a Suggested Authors box linking to matching researchers that have an ORCID iD. The box displays up to the two most prolific researchers and links to their Author Profile page. Currently, there are over 600,000 biomedical researchers life science researchers actively publishing and using their ORCIDs, having claimed about 4.7 million articles available in Europe PMC.

We have also made it easier to manage your accounts in Europe PMC. User accounts allow you to save frequently run searches. You can sign in using your ORCID, Twitter, and Europe PMC Plus credentials, or create a separate Europe PMC account. If you have several accounts due to multiple sign-ins you can now merge them to have all your saved searches in one place.

Integrated research data

Data integration is a unique feature of Europe PMC. To help researchers navigate the data-rich literature we have developed the SciLite tool. It highlights text-mined biological terms (annotations) in scientific articles and links them to related data records in public resources. Since its launch in July last year, the SciLite application has expanded to cover both abstracts and open access full text articles. The list of SciLite annotations has also broadened with the new providers joining the scheme. In addition to core named entities (gene/protein names, organisms, diseases, chemicals, Gene Ontology terms, database accession numbers), phosphorylation events, and gene functions, users can find gene-disease associations from Open Targets and DisGeNET, as well as protein-protein interactions from the IntAct database. We have added a new feature to the SciLite tool and you can now see a list of individual terms for each annotation type.

To make it easier to access all primary data associated with a study, Europe PMC has integrated with the BioStudies database. BioStudies acts as a data container, combining supplemental data and linked data residing in public repositories in a single location. Linked data is identified by text-mined accession numbers for over 20 major data resources in the life sciences, including ENA, PDBe, and UniProt. Over a million Europe PMC articles now have corresponding BioStudies records, which can be explored by clicking on the BioStudies link on the abstract pages.

Support for text and data mining

We want to make the most of having 1.8 million open access articles and 4.5 million full text articles in Europe PMC. We encourage text mining groups and developers to develop new technologies, which can improve information retrieval and researcher workflows. All open content in Europe PMC can be accessed via APIs or via the FTP site. This year we have added the literature-data crosslinks and supplementary data files (including figures for open access articles) to the list of content available for bulk download. We have also expanded the Europe PMC programmatic tools suit with the Annotations API, which allows retrieval of all text-mined annotations from Europe PMC and other providers. The API provides the means for a wider community of biomedical scientists to exploit the results of text-mining in their own research.

User community

We envision Europe PMC as an innovation platform, open for new developments coming from the community itself. We continuously undertake outreach and engagement efforts to foster a collaborative community of Europe PMC users and stakeholders. We have expanded Europe PMC user support with online training covering different aspects of the service, from literature and data search to programmatic access. We have set up a public developer forum for discussions, questions and suggestions about Europe PMC web services. Join the group to connect with the Europe PMC developers and other power users.

Among other community news, our family of 28 funders was joined by the Wellcome Trust/DBT India Alliance, who became a member of Europe PMC so that the research they fund can be archived in Europe PMC, supporting their open access policies. Over 2300 grants have been added by our funders since the spring and the database now includes more than 60,000 grants, crosslinked to the articles they supported.

It is critical to us to understand the needs of our user community and their goals, and manage Europe PMC services accordingly. At the beginning of this year we conducted a user research study to gain a better understanding of literature search behaviour and published a user research report. In the Summer we conducted a user survey with over 300 participants. The feedback we have received from the user research and survey will inform next year’s development.

After looking back at Europe PMC accomplishments, we are looking forward to the new and exciting goals for 2018. You can see what’s in store for 2018 on the Europe PMC roadmap. As always, we welcome your feedback. Leave a comment, send us an e-mail, or connect with us via Twitter. We wish you all 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.