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.

Europe PMC in 2019: a year review

As we enter a new year, let’s look back and recall the main achievements and the new features implemented in Europe PMC in the last year.

Services for users

Last Spring, we released a new version of Europe PMC plus, a service that allows  Principal Investigators supported by the Europe PMC funders to make their accepted manuscripts freely available on Europe PMC and PubMed Central.  The new Manuscript Submission System was designed to simplify and improve usability, making science more open. The new system was built using open source software as a result of the partnership with the Collaborative Knowledge  Foundation (Coko), eLife, Hindawi and others. Read more in this previous blog post: https://bit.ly/2NdfKiK.

Europe PMC also released the Funders Dashboard, which displays the profile and impact of the research publications supported by Europe PMC funders. The Funders Dashboard allows funders to check the number, availability and impact of research publications they have funded in Europe PMC, to monitor compliance with their Open Access policies. The impact section includes the total number of citations of these publications over the years, the number of publications that authors have linked to their ORCID accounts and the number of articles for which there is a preprint version.

Full-text searching and browsing 

Europe PMC ‘s final release last year was the search and article page redesign. The new design allows users to refine their literature searches by applying filters for  content type, full text availability and publication date. The new article page combines the previously separate abstract and full text pages and a figure preview appears just below the abstract. Access to the data behind the article, reviews, protocols and other useful information is available on the page, allowing for easy navigation through the article. Read more about the new Europe PMC in this previous blog post: https://bit.ly/36ALd68.

The new search functionality “did you mean?” has been introduced to assist when search terms are misspelled.  For example, if “lukemia” is typed into the search box, the “did you mean” option will offer a user the option of selecting search results for the search term “leukemia”.

Content enhancement

2019 was also a year of content enhancement. In the preprint landscape, Europe PMC welcomed medRxiv as a new preprint server, and by indexing its preprints, speeds  access to research in medical, clinical, and related health sciences. Furthermore, versioning was implemented, which displays and gives users access to preprint version history.

Europe PMC also integrated microPublications, an emerging genre of rapidly-published research communications, which allows users to find small sets (often single), validated results that include novel findings. Read more about microPublications in this previous blog post: https://bit.ly/2QD5D91.

Linking publications to the data behind them, allows readers to follow the development of an initial hypothesis and speeds scientific discovery. Last year was marked by the increase in the number of publications in Europe PMC that link- to data - this was possible due to the partnership with nearly 20 new data resources enrolled in Europe PMC’s External Links service.

Supporting text and data mining

In the text mining context, Europe PMC established the Annotation submission system, allowing text mining providers from different sources to share their annotations in Europe PMC. Additionally, the search for annotations was optimised by the implementation of the annotation tab in the advanced search option, where users can search by the type of annotation and/or by the annotation provider.

User community

 Last year was marked by some very positive interactions with the Europe PMC user community. In May 2019, Europe PMC hosted the JATS-Con conference on the use of Journal Article Tag Suite (JATS) in publishing workflows, opening discussion over the changing face of journal publishing. Following that, on-site training showed how to use Europe PMC to find evidence in research publications and reached wet-lab researchers, curators, bioinformatics and librarians from diverse institutions over Europe.

2019 also brought the Europe PMC team closer to its API user community. To highlight API use cases, Dr. Magnus Palmblad demonstrated in a webinar how he used Europe PMC to integrate publications into bioinformatics analyses and use this to generate, for example, geospatial maps showing sites of tropical disease research.

The release of the series of blog posts “Using Europe PMC APIs” enabled users to demonstrate how their work was advanced by using Europe PMC APIs eg read how Europe PMC API was integrated into a browser extension that links biomedical terms online to relevant publications ( https://bit.ly/2smKJBK), and how PDBe uses Europe PMC APIs to expose literature metadata (https://bit.ly/35Psget).

An evaluation of the value and impact of Europe PMC published last summer showed that Europe PMC has a global reach with both monetary and non-monetary value to funders and the research community. “Users identified Europe PMC as easy to use, with good coverage of content and volume, and free access to full-text publications and APIs”.

Europe PMC services are built according to users need and goals. The team are pleased to have successfully implemented changes that are sure to improve user experience of Europe PMC. The team will work to make 2020 as fruitful and are counting on user feedback and suggestions. Please feel welcome to check Europe PMC’s road map and leave a  comment or email. Programmatic users can subscribe to Europe PMC’s developer forum to leave questions. Connect with the team via Twitter and help to share the developments at Europe PMC in this new year.