Monday, 20 January 2020

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.

Wednesday, 15 January 2020

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.

Wednesday, 4 December 2019

The new Europe PMC is here

It’s time to embrace change. Today Europe PMC proudly unveils a new website, packed with useful features. The improved Europe PMC offers a better search and reading experience, as well as better access to data.

Intuitive search for articles and preprints

It’s now easier to browse search results with an optimised layout. Actions, such as saving a search or exporting citations, are displayed to the right, search filters for content type, free full text and date to the left, access menu at the top, and the list of results in the main view.
Filters allow you to limit your search to primary research articles, literature reviews, or preprints, and content labels make it easy to navigate the list of publications. 

Figures and data at your fingertips

All of the content related to the article is served on the same page, including the abstract, full text, data, and other useful resources. We wanted to put special emphasis on access to data, making it easier to get an overview of the key findings. This is now supported by two dedicated sections: figures and data. You can get to the section of interest using the left-hand navigation menu.
Figures for the open access articles are now available to preview directly under the abstract. You can view them as thumbnails, click to get an expanded view including the figure legend, or use the full text link to view a figure of interest in context.
The Data section is the go-to place for all research data associated with a study. It contains links to supplemental, supporting, and related or curated data. 
Supporting data combines data accessions and DOIs for over 40 different life science databases, including ENA, PDBe, Uniprot, and many others. The related data section lists data curated by expert groups. For example, articles with links to Disprot contain information about intrinsically disordered proteins. All data mentions are linked to external resources, where you can find more information about the data itself.
It is also possible to view data citations in the full text using the “View key terms” tool on the right-hand side. It allows you to find key terms within the text, including accession numbers and data DOIs.

Enriched publications

We have collaborated with nearly 60 different providers to link preprints and peer reviewed publications to useful resources that provide free access to peer reviews, recommendations, protocols and materials, lay summaries and more.
For example, the Reviews section will house post-publication peer reviews and scientific commentaries, while the Protocols and Materials section includes additional information about cell lines, reagents or methods used in the article.
We have also reimagined the Impact section, which now contains not only traditional article citations and alternative metrics, but also data citations, which reflect curated references from life science databases, and article recommendations by experts

Learn more

To help you explore the new features we will be releasing a series of how-to videos highlighting the changes we have described. The videos will be available on the Europe PMC YouTube channel and on the Europe PMC Help page.
You can also sign up for one of our free online webinars to learn how to find research that you should not miss. Register your interest with helpdesk@europepmc.org and we will notify you about future training events. 
If you have any thoughts or ideas regarding the new Europe PMC website, or if you would like to take part in future usability testing sessions, please let us know! Get in touch via helpdesk@europepmc.org. We hope that with your help we will continue to create the best tools for literature research.

Thursday, 19 September 2019

New science in Europe PMC: welcome microPublications

More papers are being published now than ever before. Not only that, but the sheer amount of data that goes into the publication has also increased dramatically [1]. Coupled with longer publishing times and preference for exciting findings, this makes it less likely for individual findings, even of a high scientific standard, to see the light of day.

Micropublications are meant to combat this problem, by offering a platform to share single, validated results that include novel, negative and/or reproduced results, as well as findings which may lack a broader scientific narrative. Europe PMC teams up with microPublication.org to bring this novel content to a wider audience. You can now find the full text of brief research communications from microPublication Biology alongside other peer reviewed articles and preprints in Europe PMC. 

Each article of a microPublication journal is open access, peer-reviewed and citable via a DOI. Most importantly, the data contained in the microPublication is curated and deposited to appropriate life science databases, such as WormBase.

Summary of the data submission process and validation pipeline for microPublication Biology [2].
In Europe PMC these microPublications are integrated into the search, citation network, text-mining pipeline, ORCID claiming and other tools and services.
Full text of a microPublication article in Europe PMC [3].
Supporting innovation in scholarly communications is part of Europe PMC’s mission. We hope that including micropublications will bring more valuable open scientific findings to the attention of readers. 
1. Vale RD. Accelerating scientific publication in biology. Proc Natl Acad Sci USA. 2015 Nov;112(44) 13439-13446. PMC4640799.
2. Raciti D, Yook K, Harris TW, Schedl T, Sternberg PW. Micropublication: incentivizing community curation and placing unpublished data into the public domain. Database (Oxford). 2018 Jan;2018. PMC5836261.
3. Bowles A, Wynne D, Kenton R. Vibrio vulnificus iron transport mutant has normal pathogenicity in C. elegans. microPublication Biology. 2019. CTX:M1052

Tuesday, 20 August 2019

Using Europe PMC RESTful APIs

What is FAIR-biomed?

FAIR-biomed is a browser extension that aims to facilitate investigative research in biomedicine. It connects users to information stored in specialized databases. For example, when reading an online report, with simple clicks, FAIR-biomed can help you find all the relevant information on biological entities present in that report. For example, a gene, its description, along with its biological functions and interactors. It also provides links to the sources where this gene was mentioned from the biomedical literature. 
FAIR-biomed retrieves this information from several relevant data sources including Europe PMC, NCBI, ChEMBL, Uniprot and etc. Thus, this browser extension can query entities such as genes, chemicals, pathways, authors, titles of journal articles, and other relevant and useful biomedical terms. FAIR-biomed is available on the Chrome web store and its source code is available on GitHub. This tool was developed by Tomasz Konopka from Queen Mary University of London.

As an example scenario, imagine reading a page describing a work where the development of Plasmodium parasites stopped in female mosquitoes treated with an antimalarial drug. So, if you would like to know what is new in the domain of antimalarial compounds, FAIR-biomed would allow you to access relevant published articles without needing you to switch browser tabs or even searching explicitly in the Google. Just with few clicks, select the text “antimalarial compounds”, open a context menu and select the extension with a right-click, or press Ctrl+Shift+Z on the keyboard. Voila, a pop-up window will appear, displaying all the relevant data resources, including publications from Europe PMC.


How is Europe PMC API integrated in FAIR-biomed?

FAIR-biomed sends a request to the Europe PMC servers via their  RESTful API. The top 8 results including links to the article as well as the full search results are then retrieved from Europe PMC APIs, seamlessly and very easily. Integrating this functionality was straightforward as the API endpoints at Europe PMC have an intuitive structure. The documentation is very well written and concise providing easy-to-use examples with code snippets for integration.


The browser extension is optimised to display a small set of relevant hits and therefore uses some non-default settings such as “resultType=lite” and adjusting the “pageSize=8”. All these optimised settings from Europe PMC, along with the API documentation with concise descriptions for all advanced options made the integration with FAIR-biomed a very easy task.


Try it yourself! This is the Europe PMC API query used for finding relevant information on the “antimalarial compounds”: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=antimalarial%20compounds&format=json&pageSize=8&resultType=lite 
Technically this query is a combination of strings. The API url string is stored within the extension code, and the user query is inserted in between “search?query=” and “format=json”.
The extension displays the exact API call on the “</>” icon in the bottom toolbar. So the results are reproducible! This is handy if you want to use similar API calls in your own code without reading through documentation pages. 


The extension converts JSON data from the API response into HTML paragraphs. It uses the following fields: “title”, “authorString”, “journalTitle”, “pubYear”, “pubType”. Below, is an example of the output obtained from the Europe PMC API.


By using Europe PMC APIs, FAIR-biomed allows readers to explore biomedical publications such as recent preprints, as well as peer-reviewed articles, and thus provides up-to-date information on the current literature on any biomedical topic.

Tuesday, 9 July 2019

Measuring the value and impact of Europe PMC

The value and impact of Europe PMC were recently evaluated by the independent policy research and consulting organisation, Technopolis, to assess how the platform has been serving the research community. The evaluation was based on document review, surveys, user data and interviews.

Who uses Europe PMC, what for and why?

Europe PMC has a global reach with nearly 12 million unique devices accessing the site in 2018 alone. The users are predominantly researchers, students and health professionals, who mainly use Europe PMC as one of several tools to find scientific publications. In the surveys, 87% of users found the platform useful, the preferred features being ease of use, good coverage in terms of both content and volume, and free access.

What is the economic value of Europe PMC?

Although we know it is positive, it is difficult to put a quantitative value on the benefit of integrating several services in one place. Surveys showed that individual users were willing to pay on average about $28 per year for Europe PMC while librarians proposed to pay an average fee of around $1 per user per year. Monetising the time spent by users on Europe PMC has to account for the fact that many Europe PMC functionalities could be replicated by other services. This redundancy relates to the inherently 'open' nature of much of the data and content that Europe PMC is built on, which can be freely reused by other tools and services. The final calculation resulted in values between $6 and $31 per user per year (estimating between 95% and 75% of Europe PMC that could be replicated elsewhere). While these valuations do not represent a genuine market price and the approaches used may be subject to biases, they certainly suggest that Europe PMC presents significantly higher value to users relative to the moderate running cost, which is equivalent to about $0.33 per user per year. The value thus returned to the user community for every dollar invested in Europe PMC is shown in the figure below.

How does Europe PMC benefit the biomedical research community?

Europe PMC combines several functionalities under one umbrella, such as ORCID linking, a grant finder tool, data behind a paper, open citation counts, a manuscript submission system and a number of APIs and bulk download options to access the content. It has helped further the Open Science agenda by integrating freely available research content, from full text open access research articles to preprints, books, and clinical guidelines. Finally, it provides a mechanism for funders to more readily meet their open access commitments. As such, it could play an important role in the context of Plan S. An additional key benefit of Europe PMC is its autonomy, providing a level of immunity from potential political and commercial priorities. This enables the platform to be genuinely independent and respond quickly to user needs.


Loss of Europe PMC is likely to disproportionately impact under-resourced users (e.g. researchers in developing countries and citizen scientists) who largely rely on open access to keep abreast of the latest research findings. The 29 international funders who use the platform as their open access repository would also incur additional costs in locating and using alternatives. In addition, many third-party developers who use the Europe PMC APIs would have to substantially rebuild their applications, which would require additional time and money.

Take home message

Overall, Europe PMC delivers excellent value – in both monetary and non-monetary terms – to funders as well as the global research community. Loss of such a platform would be a blow to the emerging Open Science agenda which is gaining significant momentum in recent years.

The full report can be accessed here. Please send questions related to the evaluation process to the Open Research team at Wellcome at openresearch@wellcome.ac.uk.