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 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. 

Tuesday, 12 January 2021

Research Square’s Full-text COVID-19 Preprints Now Indexed in Europe PMC

More than 4,500 Research Square preprints discoverable alongside peer-reviewed research

Research Square’s collection of more than 4,500 full-text COVID-19 preprints have been indexed in Europe PMC, an open-access repository of more than 1 million biomedical research works.

The overall effort, jointly supported by Wellcome, the UK Medical Research Council, and Swiss National Science Foundation, expands Europe PMC’s collection of more than 13,000 full-text COVID-19 preprinted research manuscripts in HTML format, and it allows the research community greater access to this COVID-19 research.

“COVID-19 has connected science and publishing in unprecedented ways, and the urgent need to share research immediately has fueled an important need for preprints,” said Michele Avissar-Whiting, Research Square Editor in Chief. “Europe PMC is doing an excellent job of fulfilling scientists’ needs through its full-text repository of preprinted COVID-19 research.” 

Since 2018, Europe PMC has indexed more than 200,000 preprints alongside its collection of peer-reviewed and journal-published articles. Similar to other articles in Europe PMC, these preprints are linked to data behind the paper, can be claimed to an ORCID, included in citation networks, and linked to comments or open peer reviews.

"Being able to access full-text preprints and peer-reviewed articles on COVID-19 in one place, and within the context of related life-sciences publications, will provide better support for research in this area", said Jo McEntyre, Associate Director of EMBL-EBI and Head of Literature Services.


About Research Square

Research Square, a division of Research Square Company, exists to make research communication faster, fairer, and more useful. Our industry-leading preprint platform, launched in 2018, is a  large, author-centric preprint server that brings transparency to the peer review process. Through our journal-integrated In Review service, innovative author dashboard, manuscript assessments, and research promotion services, we enable researchers to establish the primacy of their work, share it with the broader community, and receive useful feedback much earlier in the publication process. By improving the way science is shared, we accelerate the pace of global discovery and advancement. 

For more information on our platform and research promotion services, visit

Contact: Phillip Bogdan, Communications Manager 

About Europe PMC

Europe PMC provides comprehensive access to trusted sources of biomedical literature, all available in a single search, by indexing the metadata and abstracts of about 38 million journal published articles, reviews, preprints, micropublications, books, patents, and guidelines. Europe PMC supports the research community by developing tools for knowledge discovery, linking publications with underlying research data, and building infrastructure to support text and data mining. The Europe PMC goal is to create a supportive environment around open access content and data, to maximise its reuse.

Contact: Europe PMC helpdesk

+44 (0) 1223 49 41 18

Source press announcement: Research Square’s Full-text COVID-19 Preprints Now Indexed in Europe PMC

Wednesday, 11 November 2020

Enriching Europe PMC publications with Metagenomics annotations

We are excited to announce the recent release of metagenomics annotations for Europe PMC publications. Thanks to our joint work with MGnify on the EMERALD project, recognising metagenomics key terms in literature can now provide detailed biome descriptions for unravelling microbial implications in a variety of environmental-, engineered- and host-associated phenomena. Using a mixture of a literature-based machine learning (ML) and natural language processing (NLP) approaches, terms pertinent to 16 novel metagenomics concepts were identified in Europe PMC literature. Those concepts cover entities related to biome sample and origin as well as metagenomics experimental methods, and are all available in the Europe PMC annotations platform. Check the table below to learn about these concepts (annotation types) and their descriptions.

Annotation type



The organism where the microbiome is found


Microbiome's man-made environment


Micrbiome's natural environment


Sampling date


Microbiome's place or geocoordinates


Microbiome's site within place


Host body region/structure where microbiome is found


Host/Environment state


Sample from which the microbiome is extracted


Host/Environment treatments


Nucleic acid extraction-kit


Target gene(s) (e.g. hypervariable regions of 16s/18s rRNA gene)


PCR primers


Library strategy (e.g amplicon, whole metagenome)


Library construction method (e.g. paired-end, single-end)


Sequencing platform

Publications with the new annotations are searchable on Europe PMC using the search syntax (ANNOTATION_PROVIDER:"Metagenomics"). Entity types can be highlighted in the text of open access articles using the SciLite annotations tool.

Additionally, these annotations are available for programmatic access via Europe PMC search and annotation APIs. 

Explore metagenomics annotation types in Europe PMC and give us your feedback. Want to know more about Europe PMC annotation platform? Get in touch with

Tuesday, 22 September 2020

Announcing the new version of SciLite - the Europe PMC tool for highlighting annotations

This month, Europe PMC released a new version of SciLite, a powerful tool for highlighting annotations in life sciences publications. SciLite is powered by the Europe PMC annotation platform via the open annotation API, which provides access to over 1.3 billion annotations. Highlighting annotations in the text enables users to easily scan the article and locate key biological entities, such as genes/proteins, accession numbers, protein interactions, diseases, gene-disease relationship and more.

SciLite annotations has been redesigned to improve the speed of information retrieval and assist scientists and database curators to scan articles, extract facts and evidence from the biomedical literature, as well as locate the primary data cited in a given publication. Imagine yourself being able to locate and quickly visualise a protein structure of your interest on a single page! This is how SciLite helps with speeding scientific discovery.

Annotations can be accessed via the ‘Annotations’ option on the right-hand side on the article page. Clicking on ‘Annotations’ opens a new panel and selected terms will be highlighted in the text of the article. Notice that annotations can only be highlighted on articles with an open access license. 

The new SciLite version includes new annotation types, a new annotation panel interface and new features. Annotation types now include cell, cell lines, clinical drugs, molecular processes, organ tissues, pathway, anatomy and phenotype. The new panel offers easy navigation through annotations and displays a popup window with a quick link to relevant data resources.

Additionally, the new version offers a chemical structure viewer. Readers are able to visualise protein and chemical structures in the annotation panel as well as in the highlighted text.

Highlighted annotations display links to relevant database records enabling users to locate the primary data in the text by linking text mined and curated bioentities to public life sciences databases. Additionally, the new improvements include options to endorse, report errors or share the annotation via a linkback URL.

Identifying a plethora of complex biological terms and concepts in publications was made possible due to a successful partnership with a variety of text mining groups that use text mining algorithms to identify different types of biological entities, and enable text miners to showcase their work to a wider public via SciLite annotations. 

Europe PMC acknowledges all the annotation providers for cooperating towards submitting their annotations and welcomes new contributions from text-mining and curation communities to share annotations via the annotations submission service. Europe PMC would also like to thank all the participants who took part in usability sessions, to test and feedback on the improvements to the Scilite Annotations tool.

Want to know more about SciLite, annotation APIs or submitting annotations? Get in touch with