Tuesday, 9 February 2021

Over 15,300 full text COVID-19 now available in Europe PMC

In July 2020, Europe PMC began indexing the full text of COVID-19 preprints. The initiative supported by Wellcome, the UK Medical Research Council, and Swiss National Science Foundation, has now made over 15,300 full text COVID-19 preprints searchable and free to read, alongside peer reviewed articles.



Number of full text COVID-19 preprints in Europe PMC by month.


Researchers can benefit from a greater number of results being returned for each query since Europe PMC search tool searches not only the abstracts but also the full text of articles and preprints. The full text of COVID-19 preprints are available for reading and reuse via a standard XML format, so if a preprint has an open license, it can be text mined programmatically, allowing deeper analysis of the COVID-19 literature.

Which servers are indexed?

Europe PMC currently indexes full text COVID-19 preprints from biomedical servers bioRxiv, and MedRxiv.  Adding to this, Europe PMC also includes full text COVID-19 preprints from Research Square, ChemRxiv, SSRN and from arXiv.


Preprint server

Disciplinary scope

arXiv

Multiple scientific fields, including quantitative biology

bioRxiv

Broad life & biomedical research (from animal behaviour and cognition to zoology)

ChemRxiv

Subject-specific, including biological and medicinal chemistry

medRxiv

Broad medical, clinical and related health sciences

Research Square

All scientific fields

SSRN

Multiple scientific fields including applied sciences, health sciences, life sciences, social sciences

Disciplinary scope was taken from ‘Preprint server directory’ at https://asapbio.org/preprint-servers 


 

Europe PMC uses the PDF freely available on these preprint servers to create the full-text HTML version of the preprint, which is later sent for author approval to display by Europe PMC.  A single query will access 15,000 preprints from across these 6 servers.

 

Number of full text COVID-19 preprints in Europe PMC by preprint server.

 

 

 

Data re-use

One of the aims of the project is to provide a unique corpus of COVID-19 research for current and future research. The COVID-19 full text articles in Europe PMC have already been used for data analysis in the following studies:


 

Future plans

Europe PMC is planning to index full text preprints from Preprints.org, Authorea and other preprint servers and platforms which include relevant COVID-19 content. To see an updated list of preprint servers check the ‘About preprint page’ on Europe PMC website.




For more information about preprints in Europe PMC, visit our website: https://europepmc.org/Preprints



Tuesday, 19 January 2021

Europe PMC announces renewed funding and two new funders join the family

 

Europe PMC infrastructure grant renewal


We start 2021 with the exciting news that the Europe PMC infrastructure grant has been renewed for the period April 2021 to March 2026. The grant award is supported by 30 international biomedical funders and led by the Principal Investigator Dr Johanna McEntyre, of the European Bioinformatics Institute (EMBL-EBI). The grant enables the continued development and maintenance of the Europe PMC infrastructure and supports the Open Access policies of the Europe PMC funders, by enabling researchers to self-archive journal articles.


"I am delighted that funding for Europe PMC is secured until 2026. This will allow Europe PMC to not only support the open access policies of the Europe PMC funders, but also provide comprehensive free and open access to  research abstracts, full text and preprints. Europe PMC is a community resource, and a key part of European and global data infrastructure, providing vital links between data and articles to support open science”, said Jo McEntyre, who is also Associate Director of EMBL-EBI and Head of Literature Services.

Two national funding organisations in the Netherlands, NWO and ZonMw, join Europe PMC


We're excited to announce that the NWO and ZonMw join Europe PMC’s funder family this year.


The Netherlands Organization for Scientific Research (NWO), funds interdisciplinary, curiosity-driven research that is focused on societal challenges and also invests annually in research infrastructure. Notably, The NWO announced its Open Science fund in December 2020, a programme that will support researchers in developing, testing and implementing innovative ways of making research open.



ZonMw funds the full spectrum of healthcare research, from basic research to the implementation of new treatments, disease prevention, and health care improvements in the Netherlands,  as well as contributing to international programmes. ZonMw works closely with the NWO, with their focus on healthcare research complementing NWO’s support of a wider range of scientific research areas.


Researchers funded by NWO and ZonMw will join thousands of others who make their published research articles freely available from Europe PMC as soon as possible. Both national funders are supporters of Coalition S meaning that all published research articles funded by NWO and ZonMw grants that are awarded from January 1st 2021, should be made immediately available for reading and reuse through Europe PMC, without embargo. 



For more information about joining Europe PMC as a funder, visit our website: http://europepmc.org/Joining


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. 


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 researchsquare.com.

Contact: Phillip Bogdan, Communications Manager

phillip.bogdan@researchsquare.com 

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

helpdesk@europepmc.org



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