Thursday, 14 January 2021

Europe PMC in 2020: a year review

The year 2020 was marked by the global COVID-19 pandemic and the Europe PMC team, like many others around the world, started to work from home. Scientific literature is at the heart of scientific research and during these extraordinary times, Europe PMC worked on improving existing services, building new features, increasing the full text content by including the full text of COVID-19 preprints and improving full text browsing, supporting text and data mining and engaging with the Europe PMC community. Despite the circumstances, 2020 was a busy year for Europe PMC, so let’s look back at the main achievements and the new features implemented in Europe PMC last year.

Service for users

2020 was a year of great partnerships! Europe PMC partnered with Scite to integrate smart citations on the Europe PMC platform. These smart citations provide the excerpt of text surrounding the citation, the section of the article in which the reference is mentioned, and indicates whether the citing study provides supporting or disputing evidence. Users can easily find smart citations in the Citations & Impact tab of the articles for which smart citations are available. Read more about smart citations in Europe PMC here.



Europe PMC also partnered with the Medical Research Council (MRC), the UK Collaborative on Development Research (UKCDR) and the Global Research Collaboration for Infectious Disease Preparedness (GLoPID-R) to make COVID-19 grant data more widely available via the Europe PMC COVID-19 grant finder. Over 2,127 grants from 27 international funders have been included. Read more here.


It is now even easier to link an article to the ORCID profile with the new ORCID claiming button implemented on the Europe PMC article page. 

Europe PMC also supported researchers funded by Europe PMC funders to comply with Plan S by implementing new functionality in the Europe PMC plus manuscript submission system. 

Full text searching and browsing

In 2020, Europe PMC also made improvements to preprint versions, aggregating all versions of a preprint together and displaying only the most recent versions of a preprint in the search results. Users can navigate through different preprint versions by using the preprint history menu. Read more here.

Europe PMC links preprints to the peer reviewed version of the article if it is available in Europe PMC. Last year, finding published versions of preprints was made easier by the new search functionality for preprints, the “published version” filter.

As a response to the COVID-19 pandemic, Europe PMC also implemented a COVID-19 search banner to make it easier for users to find the latest COVID-19 related articles. The yellow banner can be found on top of Europe PMC web pages.

Content enhancement

During the COVID-19 pandemic, researchers have published results rapidly, usually through preprints. In July 2020, Europe PMC supported by Wellcome in partnership with the UK Medical Research Council (MRC) and the Swiss National Science Foundation (SNSF), started to index full text COVID-19 preprints. This initiative has made over 13,000 full text COVID-19 preprints available for reading and reuse via a standard Journal Article Tag Suite (JATS) XML format, alongside peer reviewed full text articles. The preprints with an open license can also be programmatically accessed and downloaded for text mining, allowing deeper analysis of the COVID-19 research landscape. Read more about this initiative here.

Europe PMC collaborated with additional preprint servers. Preprint abstracts from Beilstein Archives, Research Square, SSRN and Authorea are now searchable in Europe PMC as well as the full text COVID-19 preprints from bioRxiv, chemRxiv, medRxiv, Research Square and SSRN.

Supporting text and data mining

Europe PMC also welcomed three new annotation providers: OntoGene, PheneBank and Metagenomics (EMERALD) which provide annotations on cell, cell lines, clinical drugs, molecular processes, organ tissues, pathway, anatomy, phenotype and metagenomics concepts. Users can now find over 1.3 billion annotations covering 42 different annotation types in Europe PMC.

SciLite annotations, the powerful tool for highlighting annotations in Europe PMC, gained a new look in 2020. The new version of SciLite includes new annotations types, a new panel interface and improved features such as the chemical and protein structure viewers that allow readers to visualise and interact with the structures directly on the article page. 

User community

Early last year, Europe PMC connected with the Europe PMC API community to release an API use case page where programmatic users can share the applications they have created using Europe PMC APIs.


In March 2020, Europe PMC released a video showing how different users such as researchers, policy makers, biocurators and innovators use Europe PMC.



Europe PMC continued to run regular webinars on various aspects of Europe PMC. We appreciated the questions and feedback we received from many attendees.


“I learned about Europe PMC and the way it is connected with databases such as OMIM, ENA, InterPro, Mouse genome informatics, etc.” 


“The Europe PMC is really comprehensive and fun to use”


“It was informative as I never used Europe PMC. Thanks”


Europe PMC participated in the eLife Innovation Sprint 2020 working on the projects convidpreprints.com and Annotate them all.  In mid September, the team also participated in the conferences Reproducibility, Replicability and Trust in Science (RRTS20) and OASPA2020 with posters and lightning talk on ‘Full text COVID-19 preprints in Europe PMC’, ‘Connecting research resources  - building the PID Graph in Europe PMC’ and ‘Global Grants DOIs in Europe PMC’.  


Last November, Europe PMC open-sourced Text-annotator, a JavaScript library to locate and annotate plain text in HTML. Text annotator is used in Europe PMC to highlight article title, snippets and biological entities via SciLite annotations. Read more here. The Europe PMC team also published the article ‘Europe PMC in 2020’ giving a snapshot of what Europe PMC has to offer researchers.

 

Europe PMC is glad to have been able to develop and implement new features to support users' needs in 2020. The team will continue to make it easier for users to read and extract information from the scientific literature in 2021.


If you are interested to find out what we will be working on in 2021, take a look at Europe PMC’s road map and leave a comment or email us if you have questions.

Connect with us via Twitter and help to share the developments at Europe PMC in 2021. Programmatic users can subscribe to Europe PMC’s developer forum to leave questions. 


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