Europe PMC to include the full text of COVID-19 preprints

In this pandemic, researchers have responded by publishing results rapidly, often through preprints.

In fact, up to half of the publications in Europe PMC on COVID-19 are preprints rather than peer-reviewed journal articles. Currently, the full text of these preprints are scattered as PDFs on preprint servers, or, available as a non-standard set of documents for machine learning purposes. 

In a new project, supported by Wellcome in partnership with the UK Medical Research Council (MRC) and the Swiss National Science Foundation (SNSF), we will make the full text of COVID-19 preprints available on Europe PMC, a large and sustainable life sciences archive, for reading and reuse via a standard XML format, alongside peer reviewed full text articles. 

“Being able to easily search and read preprint full text on a site already frequented by millions of users means that they will be significantly more discoverable by people, and more open to scrutiny”, says Jo McEntyre, Associate Director of EMBL-EBI and Head of Literature Services. “We will make use of existing infrastructure to integrate these COVID-19 preprints into the typical ecosystem of publications - for example, linking to the underlying data”.

This will accelerate scientific research on COVID-19, provide an opportunity to build new open and rapid publication systems, and form a corpus for future history of science research.

"The COVID-19 pandemic has the potential to be the "Napster moment" for preprints, which in turn could herald a way in which research outputs are shared in the future.  Ensuring preprints are fully discoverable and reusable will help ensure that they are treated as first class research objects.  This initiative to make them fully discoverable through the Europe PMC repository will help to realise this goal."

Said Robert Kiley, Head of Open Research at Wellcome

In the coming weeks and months, we will be engaging with preprint servers and preprint authors to make as many COVID-19 preprints as possible available for reading and reuse via Europe PMC. If you are the corresponding author on a preprint on SARS-CoV-2 or COVID-19, published on one of the major preprint platforms, we will soon be asking you to review the Europe PMC version of your work.

Europe PMC has been indexing preprint abstracts since 2018 and has the experience in managing full text workflows at large scale. A total of approximately 150K preprint abstracts currently sit among all of PubMed (31M abstracts) and 6M full text articles shared with PMC in the USA. These are XML-based workflows based on international standards (JATS). Europe PMC has played a leading role in preprint community standards development and has hands-on expertise in publication workflows that include versions across multiple sources with diverse approaches.

In addition, Europe PMC has several mechanisms to integrate related material - whether it is data behind the paper to substantiate conclusions, ORCID claiming of preprints, inclusion of preprints in citation networks, or to comments on peer review platforms, impact metrics, or links to reagents.

Jessica Polka, Executive Director of ASAPbio said:

"This exciting initiative will create a reading experience that is not only more seamless, but also potentially richer. Openly licensed documents can be text mined and enhanced with SciLite annotations, adding context for readers. The inclusion of the full text of COVID-19 preprints in Europe PMC is an important step in the integration of preprints into the scholarly communications infrastructure."

To find out more about this initiative, write to Europe PMC at: helpdesk@europepmc.org.

Global grant IDs in Europe PMC

In September 2019 we welcomed the first open, global grant IDs to Europe PMC. Wellcome became the first funder to register DOIs for their grant awards with Crossref. Grant metadata is provided by Europe PMC, and in a pilot integration, the grant IDs were featured in a PLOS ONE publication. This is a very exciting development that will hopefully make it easier to effectively track the impact of research funding. So what is the big news about?

What are grant IDs?

Open, global grant identifiers have been in the making for some time. Though grant numbers are already in use by many funders, they are often local and based on an internal pattern. 

This might create some issues when looking up grant information provided by different funders - for a grant with a local ID 207467 two records exist in Europe PMC, one awarded by Wellcome and another by the European Research Council.

One of the proposed solutions is adoption of global grant IDs in the form of DOIs, which offer the advantages of being unique, persistent, and easy to integrate into existing systems.

To create DOIs for their grant awards funders need to follow three simple steps:

• join Crossref as a member;
• register associated metadata, such as grant award title, amount, currency, date, etc;
• provide an openly available online resource to which the DOI would resolve - a landing page describing the grant.

Creating grant DOIs

As the first step in the process, Wellcome became a Crossref member through a new type of membership developed specifically for this purpose. It is distinct from the publisher membership and is designed for funding agencies. Upon registration Wellcome was assigned a unique DOI prefix.

DOI example for a Wellcome-supported grant.

For the second step, Europe PMC registered global grant IDs for Wellcome-funded awards with Crossref on behalf of the funding agency. Because Europe PMC already runs an open database of grant awards for all 31 Europe PMC funders, we were best placed to provide Crossref with the necessary metadata. 

The metadata schema is comprehensive and allows for a detailed overview of the grant. Europe PMC presents the information registered for most of the fields, including the funding percentage for grant awards supported by multiple funders, or ORCIDs for investigators on the grant (see scheme below). The full schema and documentation are available on GitHub.

Metadata fields that Europe PMC provides to Crossref when registering a global grant ID.

Greater transparency for funding information

The beauty of a DOI is that it points to a physical location, some place where an interested user can see the details of a particular grant. For Wellcome, that place is a grant record on Europe PMC’s website. This means that the funding information becomes more transparent and can be easily linked to the research output.

Example of the grant record on the Europe PMC website. This record matches the grant DOI referenced in the PLOS ONE article below.

In a pilot effort the journal PLOS ONE coordinated with Wellcome-funded authors to include newly registered global grant IDs in the metadata of the publication. This means that the readers can now seamlessly navigate from the article to the grant record and examine the support provided by Wellcome for this particular study.

Global grant IDs for two Wellcome grants featured in the Funding section of a PLOS ONE publication. The link for the first of these Wellcome grants leads to the grant record shown in the figure above.

Notably, all of this grant-associated metadata is freely available not only on Europe PMC’s website but also programmatically, through the public GRIST API. The newly created global grant ID along with the local grant number have been incorporated into the API response. The information will also be available via Crossref’s APIs later in 2020. 

Future plans

DOIs for grants have been registered on behalf of Wellcome for 237 grants awarded in 2019. Grant IDs will be assigned retrospectively to Wellcome grants awarded and registered in Europe PMC’s GRIST database from years prior to 2019. This will encompass approximately 13,500 Wellcome grants currently available in Europe PMC. 

The adoption of global grant IDs also allows us to create a more interlinked PID (persistent identifier) graph - as Europe PMC hosts data for both publications and grant awards we are well-positioned to link publication DOIs with DOIs for grants, supporting better tracking of the research funding impact. 

We hope that by implementing global grant IDs, grant data can be easily collected on submission by publishers and repositories and automatically fed into researcher assessment platforms, thereby simplifying researchers’ workflows.

For more information

Europe PMC funders, please contact helpdesk@europepmc.org if you’d like more information about registering grant DOIs. 

For more general information from Crossref please see their website.

Europe PMC’s contribution to this work has been funded by the Europe PMC funders and the European Commission: FREYA - Connected Open Identifiers for Discovery, Access and Use of Research Resources (777523)

MQ: Transforming Mental Health and Pancreatic Cancer UK join Europe PMC

We're delighted to announce that MQ: Transforming Mental Health and Pancreatic Cancer UK join Europe PMC as a new funder. This brings the Europe PMC funder family to 31 members.

MQ: Transforming Mental Health is an international mental health research charity that funds multidisciplinary research into mental health across biological, psychological and social sciences. With over 40 research projects to tackle mental illness, MQ vision is to create a world where mental illnesses are understood, effectively treated and one day made preventable.

Pancreatic Cancer UK invests in creative and cutting edge research and supports, develops and attracts the brightest minds in the field who will go on to be the leaders of pancreatic cancer research in the future. Pancreatic Cancer UK’s active portfolio of projects aim to advance understanding of the biology and to develop new strategies for diagnosis and treatment of pancreatic cancer, as well as ensuring that patients have the best standard of treatment, care and support. 

Researchers funded by MQ: Transforming Mental Health and Pancreatic Cancer UK will join thousands of others who make their published research articles freely available from Europe PMC as soon as possible, and in any event within six months of publication.

For more information about joining Europe PMC, visit our website: 

http://europepmc.org/Joining

Five stories showing how Europe PMC is used by the life sciences community

Europe PMC is a searchable database that allows access to life sciences publications worldwide including preprints and micropublications. Europe PMC offers cutting-edge tools to improve the discovery of articles around a topic of interest and provides links to the data behind the articles. In a commitment to open science, Europe PMC flags articles that are free to read and even better, free to re-use. Additionally, it offers powerful APIs and easy documentation for programmatic access to the knowledgebase in Europe PMC.

Europe PMC is used by both experienced and early career researchers, policy makers, biocurators and innovators seeking to enhance scholarly publishing and more. What could be better than letting Europe PMC users talk about their experiences? Watch the video below to see how Europe PMC helps different users in the life sciences community to do their everyday jobs.

Start your knowledge discovery journey now, access https://europepmc.org and spread the word.

Making sense of preprint versions

Europe PMC has been indexing preprints since 2018, hosting content initially from bioRxiv, ChemRxiv, PeerJ Preprints, F1000, and subsequently adding content from medRxiv and Beilstein Archives. Europe PMC now indexes over 100K preprints. Through a recent redesign of the search functionality, Europe PMC  highlights more clearly search results that are preprints (versus research articles or literature reviews, for example).

However, an open question has been how to deal with the many different versions of a preprint appearing in the search results. The aim was to identify all versions of a preprint, link them together and offer a collapsed aggregate of these versions to users. To this end, Europe PMC has improved the presentation of preprint versions and displays only the most recent version of a preprint in the search result page.

https://europepmc.org/article/PPR/PPR97325

Europe PMC links preprint versions based on their DOIs, allowing the user to access previous versions along with the edits, comments and citations associated with each specific version. From each preprint version the user can also link to the peer-reviewed, published version of the article if it is available in Europe PMC.

Europe PMC supports the discoverability and trustworthiness of preprints by linking together preprints versions, the final peer reviewed publication, reviews and highlights.

Get in touch via helpdesk@europepmc.org and leave your feedback and suggestions.

Europe PMC Funders’ Dashboard

What research outputs did you fund?

Research funders need to track the outcomes of research that they have funded. To facilitate this Europe PMC has recently developed the Funders’ Dashboard, a new feature available for Europe PMC funders, which displays the profile and impact of the research publications in Europe PMC that they have funded.

How to use the Funders’ Dashboard

The dashboard for each of Europe PMC’s funders can be accessed by from the funders tab in the ‘About’ Europe PMC’s menu.  You can switch to dashboards of other funders easily by using the dropdown menu at the top right of any Funders’ Dashboard page (see below). 

Every dashboard displays interactive information graphics showing the availability and impact of research publications resulting from the funder’s grants. These are accessed via two tabs at the top of the page:

• Open Access tab

This tab provides information on the open access compliance of articles per year. Specific dates can be selected via the date picker on the right top of the chart. Europe PMC funders mandate research outputs of the research they fund to be made freely and readily available with a CC-BY license in Europe PMC, usually within 6 months of publication. This visualisation provides a snapshot of the effectiveness of a funder’s open access policies and allows for easy monitoring of compliance with specific mandates.

Making the data behind the publications freely available for reuse is an alternative way to measure the impact and transparency of research. Europe PMC funders can see the number of publications with links to supporting and related data over any selected year on the ‘Open Access’ tab of the Funders’ Dashboard.

• Impact tab

The Funders’ Dashboard ‘Impact’ tab displays the total number of citations of the publications supported by Europe PMC funders by year. Again, it is possible to select the dates of interest by using the date picker on the top right of the chart. This enables funders to access research outcomes and impact.

The Impact tab of the Funders’ Dashboard also shows the number of articles with an ORCID in Europe PMC and the number of articles with an ORCID ID for each Europe PMC funder. ORCID is a unique identifier for researchers, which by distinguishing researchers with similar names, ensures a researcher is accurately linked to a citation. By integrating ORCID-linking, Europe PMC makes it possible for authors to link their publications to their ORCID profiles via the Europe PMC website. For funders, the use of ORCID IDs makes reporting more accurate.

A third feature of the ‘Impact’ page is a graphic presenting the adoption of preprint posting by fundees. Preprints are research articles that have not yet completed formal peer-view. The number of biomedical publications being posted on preprint servers has increased over the last 10 years and some funding agencies have changed their policies to promote the early posting of research via preprints. Europe PMC indexes preprints from several preprint servers, and links preprints to the finalised journal article version where it exists. The graphic below indicates the rise in the number of articles funded by a Europe PMC funders that are based on a preprint.

Collating the information for the dashboards

To improve the discoverability of publications supported by Europe PMC funders, a text-mining pipeline was developed that identifies specific grant awards in full-text articles (learn more by reading the paper by Parkin et al. 2019). This text mining pipeline located ~85,000 full-text articles that contain Europe PMC funder grant IDs and this information is used to feed the Funders’ Dashboard.

The data used to build the dashboards are available via Europe PMC’s open APIs, allowing funders to easily retrieve the same data via these APIs or the Europe PMC search if they choose to. Using the Europe PMC open APIs makes it possible for funders or other organisations to reproduce the dashboards or develop similar applications. 

The Funders’ Dashboard facilitates the necessary tracking of published grant outputs by displaying up-to-date information graphics on the research publications funded by all Europe PMC funders. Europe PMC is proud to provide this feature for all of its funders. Please get in touch with the Europe PMC team at helpdesk@europepmc.org if you have queries or suggestions for improvement.

Europe PMC Integrates Smart Citations from scite.ai

Scite, an award-winning citation analysis platform, and Europe PMC, an open science discovery tool that provides access to a worldwide collection of life science publications, have partnered to display what scite calls smart citations on the Europe PMC platform.

Smart citations advance regular citations by providing more contextual information beyond the information that one study references another. Specifically, smart citations provide the excerpt of text surrounding the citation, the section of the article in which the reference is mentioned, and indicate whether the citing study provides supporting or contradicting evidence. As a result, one can evaluate a study of interest much faster.

Scite has been collecting the information required for smart citations from open access sources as well as through partnerships with such publishers as Wiley, the BMJ, and Future Science group and others yet to be announced. Currently, the scite database has 450M citation statements extracted from 14M publications that cite 31M articles.

To make smart citations accessible, Europe PMC will display citation analysis by scite on the Citations & Impact tab of articles for which smart citations are available. The citation analysis displays how many articles have supported, contradicted, or mentioned the article, and will be linked to a full scite citation report where users can explore the context of each citing article (https://europepmc.org/article/MED/18724357#impact).

Josh Nicholson, co-founder and CEO of scite says, “We’re happy to introduce smart citations on the newly redesigned Europe PMC website. Europe PMC has been an innovator in providing new tools to researchers to help them better discover relevant research and we think scite provides something unique that researchers will find very valuable in their literature search.”

Michele Ide-Smith, Service Coordinator of Europe PMC says, “Europe PMC is delighted to collaborate with Scite to include this novel and useful feature. As Scite Smart Citations provide a helpful summary of the citation context, we hope that it will allow researchers and scientific curators to quickly assess the impact of articles."

About scite

scite is a Brooklyn-based startup advancing citations with the introduction of smart citations. Using deep learning scite has classified 450 million citation statements from 14 million scientific articles that support, contradict, or mention prior research. scite is used by researchers from dozens of countries and is funded in part by the National Science Foundation and the National Institute of Drug Abuse of the National Institutes of Health.

For more information, please visit scite, follow us on Twitter, LinkedIn and Facebook, and download our Chrome or Firefox plugin.