The year 2021 has been difficult for many people working remotely, including those here at Europe PMC. We have been unable to meet in person with the users and the wider community that drives this service.
As this year has drawn to an end we have taken the time to reflect on some of the improvements made to Europe PMC to make the life science research even more accessible, discoverable, and re-usable.
Europe PMC continually strives to enhance the available content in line with what its users need. To address this in 2021 we focused on increasing transparency for preprints. Preprints are an excellent open resource for researchers to rapidly share scientific discoveries before journal-organised peer review. In some circumstances authors may wish to withdraw or remove their preprint. Europe PMC now provides a way to search and display withdrawn and removed preprints with appropriate labels, for the COVID-19 full text preprint subset. Currently withdrawn and removed preprints are identified in Europe PMC using a semi-automated approach, however we hope that in the future preprint servers will be able to share the preprint withdrawal/removal status as part of the machine readable metadata freely available in Crossref.
As part of Europe PMC’s commitment to open access research, over 14,000 psychological sciences preprints from PsyArXiv were added to the Europe PMC database, making the latest psychology research more accessible and discoverable.
Following the initiative to include full text COVID-19 preprints in Europe PMC since June 2020, we have continually ingested new content and are excited to announce there are now ~27,000 COVID-19 full text preprints available for search and display in Europe PMC.
We have also expanded the amount of grant—article links available on Europe PMC by adding funding data provided by publishers to Crossref. Thus improving transparency for research funding and making it easier for funders to track publications they have supported.
Service for users
We know that keeping up to date with the literature is a time-consuming process, and based on user requests we have introduced email alerts. This feature can help users keep up with current research in their field, track new publications and preprints from over 25 different platforms, and follow individual researchers, groups, and institutions, as well as journals of interest.
For those using Europe PMC APIs we have developed a status update change module that allows users to submit batches of article IDs to identify if any articles have been retracted. For preprints this feature allows users to identify if a preprint has a new version, has been withdrawn, or has been published in a peer-reviewed journal.
In 2019 the Europe PMC article and search pages were redesigned based on several user research studies. Further improvements were made in 2021, including a redesign of the Home, About, and Help pages to address common questions that the new users had about what Europe PMC is and what it offers.
With accessibility at the heart of Europe PMC, further design changes were made to ensure life sciences research can be accessed by anyone and everyone. This year we made multiple improvements to the Europe PMC website to meet UK and US government accessibility guidelines set out by the W3C. These improvements allow those using voice commands, screen readers, keyboard commands, zooming, and other assistive devices to use the website more easily. There are a variety of browser settings that can be changed to make reading content easier, including zooming up to 300% without text spilling off the screen, changing text size, contrast, colour, and fonts, making content easier to read.
We have made it even easier for the authors supported by Europe PMC funders to link their grants to articles to meet funding requirements. During the manuscript submission process in Europe PMC plus we have introduced a grant-linking step for full text articles already available in Europe PMC.
From 1st January 2021, authors supported by Horizon Europe grants or grants from cOAlition S funders are required to release their manuscripts immediately with no embargo and a CC-BY license. We made changes to Europe PMC plus to ensure authors archiving their manuscripts in Europe PMC could comply with these new open access policy requirements.
Integrated research data
In 2021 Europe PMC has partnered with two open community databases, PGS Catalog and Xenbase, to link publications with relevant curated data records. The Polygenic Score (PGS) Catalog is an open database of polygenic scores and the relevant metadata required for accurate application and evaluation of results. Xenbase is a web-accessible resource for integrated biological and genomic data for the Xenopus model organism. Europe PMC provides access to over 53,000 Xenopus-related and over 250 PGS-related publications with links to data citing the publication discoverable from the publication Data tab.
To aid the identification of the key COVID-19 papers, Europe PMC has partnered with the Swiss Institute of Bioinformatics Text Mining team to add the Coronavirus Vocabulary (COVoc) annotations based on an ontology developed by the EMBL-EBI SPOT team. This enables searches for publications in Europe PMC that contain COVID-19 ontology terms.
In a joint project between the Europe PMC and MGnify teams, Dr Maaly Nassar’s machine learning framework enriched publications in Europe PMC with metagenomics annotations. In total the framework identifies 16 different entities that describe biome origin and metagenomics methods, such as ‘Sample Material’, ‘Body-site’, ‘Kit’, ‘Primer’ and environment ‘State’. Those same annotations can be explored in the MGnify database, with the context for each term provided as a text snippet linked to the publication.
We were delighted that the Europe PMC funding was renewed for the period 2021–2026. The grant is supported by 33 international biomedical funders and is essential for the continued development and maintenance of Europe PMC’s infrastructure.
Excitingly, Europe PMC has welcomed two new funders to the funder family in 2021: the Netherlands Organisation for Scientific Research (NWO) and ZonMw. NWO funds interdisciplinary research focused on societal challenges and, as part of their commitment to open science, they also invest in research infrastructure. ZonMw funds healthcare research, with a focus on innovation, increasing scientific knowledge, and implementing these innovations and discoveries in policies and health care practices. ZonMw is an advocate for international collaboration and works closely with NWO.
The API use case page showcases projects from the Europe PMC web service user community. A new case study from the University of Virginia highlights the use of the Europe PMC REST API to study open access publishing at their institution. Using the University of Virginia’s open source code and the Articles API provided by Europe PMC anyone can apply this approach to visualise the open access practices at their own institution.
The proportion of open access versus subscription-only articles published by the UVA Health affiliated authors and indexed in Europe PMC. Visualisation created using Europe PMC API and Streamlit.
This year we have created and delivered multiple webinars and training to support users and highlight the benefits of open science. The key webinars and training to highlight are:
- The future of preprint peer review
- Preprints 101 for authors
- Analysing publications and funding with the Europe PMC REST API
Europe PMC is dedicated to continually addressing the needs of users and is proud of the new developments that have been implemented in 2021. If you are interested to find out what we are planning for 2022 please look at Europe PMC’s Roadmap and let us know what you think.