Wednesday, 15 January 2020

Europe PMC in 2019: a year review





As we enter a new year, let’s look back and recall the main achievements and the new features implemented in Europe PMC in the last year.

Services for users

Last Spring, we released a new version of Europe PMC plus, a service that allows  Principal Investigators supported by the Europe PMC funders to make their accepted manuscripts freely available on Europe PMC and PubMed Central.  The new Manuscript Submission System was designed to simplify and improve usability, making science more open. The new system was built using open source software as a result of the partnership with the Collaborative Knowledge  Foundation (Coko), eLife, Hindawi and others. Read more in this previous blog post: https://bit.ly/2NdfKiK.

Europe PMC also released the Funders Dashboard, which displays the profile and impact of the research publications supported by Europe PMC funders. The Funders Dashboard allows funders to check the number, availability and impact of research publications they have funded in Europe PMC, to monitor compliance with their Open Access policies. The impact section includes the total number of citations of these publications over the years, the number of publications that authors have linked to their ORCID accounts and the number of articles for which there is a preprint version.



Full-text searching and browsing 

Europe PMC ‘s final release last year was the search and article page redesign. The new design allows users to refine their literature searches by applying filters for  content type, full text availability and publication date. The new article page combines the previously separate abstract and full text pages and a figure preview appears just below the abstract. Access to the data behind the article, reviews, protocols and other useful information is available on the page, allowing for easy navigation through the article. Read more about the new Europe PMC in this previous blog post: https://bit.ly/36ALd68.

The new search functionality “did you mean?” has been introduced to assist when search terms are misspelled.  For example, if “lukemia” is typed into the search box, the “did you mean” option will offer a user the option of selecting search results for the search term “leukemia”.



Content enhancement

2019 was also a year of content enhancement. In the preprint landscape, Europe PMC welcomed medRxiv as a new preprint server, and by indexing its preprints, speeds  access to research in medical, clinical, and related health sciences. Furthermore, versioning was implemented, which displays and gives users access to preprint version history.


Europe PMC also integrated microPublications, an emerging genre of rapidly-published research communications, which allows users to find small sets (often single), validated results that include novel findings. Read more about microPublications in this previous blog post: https://bit.ly/2QD5D91.

Linking publications to the data behind them, allows readers to follow the development of an initial hypothesis and speeds scientific discovery. Last year was marked by the increase in the number of publications in Europe PMC that link- to data - this was possible due to the partnership with nearly 20 new data resources enrolled in Europe PMC’s External Links service.


Supporting text and data mining

In the text mining context, Europe PMC established the Annotation submission system, allowing text mining providers from different sources to share their annotations in Europe PMC. Additionally, the search for annotations was optimised by the implementation of the annotation tab in the advanced search option, where users can search by the type of annotation and/or by the annotation provider.


User community
 Last year was marked by some very positive interactions with the Europe PMC user community. In May 2019, Europe PMC hosted the JATS-Con conference on the use of Journal Article Tag Suite (JATS) in publishing workflows, opening discussion over the changing face of journal publishing. Following that, on-site training showed how to use Europe PMC to find evidence in research publications and reached wet-lab researchers, curators, bioinformatics and librarians from diverse institutions over Europe.

2019 also brought the Europe PMC team closer to its API user community. To highlight API use cases, Dr. Magnus Palmblad demonstrated in a webinar how he used Europe PMC to integrate publications into bioinformatics analyses and use this to generate, for example, geospatial maps showing sites of tropical disease research.
The release of the series of blog posts “Using Europe PMC APIs” enabled users to demonstrate how their work was advanced by using Europe PMC APIs eg read how Europe PMC API was integrated into a browser extension that links biomedical terms online to relevant publications ( https://bit.ly/2smKJBK), and how PDBe uses Europe PMC APIs to expose literature metadata (https://bit.ly/35Psget).

An evaluation of the value and impact of Europe PMC published last summer showed that Europe PMC has a global reach with both monetary and non-monetary value to funders and the research community. “Users identified Europe PMC as easy to use, with good coverage of content and volume, and free access to full-text publications and APIs”.

Europe PMC services are built according to users need and goals. The team are pleased to have successfully implemented changes that are sure to improve user experience of Europe PMC. The team will work to make 2020 as fruitful and are counting on user feedback and suggestions. Please feel welcome to check Europe PMC’s road map and leave a  comment or email. Programmatic users can subscribe to Europe PMC’s developer forum to leave questions. Connect with the team via Twitter and help to share the developments at Europe PMC in this new year.

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