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.

Tuesday, 11 June 2019

Submission system for text-mined annotations

From algorithms to the bench
Text-mining holds the promise of helping researchers to overcome information overload. It is a familiar premise: an avalanche of scientific knowledge is being produced and shared. Teaching machines to “read” might soon be the only manageable way to digest large amounts of information into useful facts.

To extract bits of information, such as biological concepts or relations, from the text, various text-mining tools have been developed in the recent years. Even as the text-mining technology becomes more widespread, an average researcher will rarely be exposed to its benefits. Scholars get to publications via a few familiar routes, which may not utilise text-mining technologies. In addition, different text-mining platforms may focus on different topics or categories: one suited for molecular interactions, another for gene-disease associations.

To address these issues, Europe PMC has established a platform that consolidates text-mined annotations from different sources and makes them available to the wider research community. The annotated concepts and relations are displayed on article pages via SciLite tool, and can be retrieved using RESTful API.


To simplify the process of sharing text-mining results Europe PMC has developed a dedicated Annotation Submission System. It allows expert text-mining providers to publish their annotations in Europe PMC. The system can also accept relevant statements manually curated by dedicated biocuration groups.

The submission process is straightforward and does not require strong technical skills. It is possible to submit an annotation file either using the web browser or programmatically. Note that for programmatic upload Cloud Storage System drivers are available in different languages.



Here is how annotation data is represented in the system:


Europe PMC Annotation Submission System accepts sentence-based annotations and named entity annotations. An example of a sentence-based annotation is a protein-protein interaction, while a chemical name can be represented as a named entity. All annotated concepts must be linked to ontologies and data resources. For instance gene/protein annotations link to a corresponding UniProt record. Submitters are also asked to specify the precise location of the annotation in the text, using prefix and postfix tags.
Such location information can be used to reciprocally link from the annotation to the relevant sentence of the article in Europe PMC via a link-back mechanism. neXtprot, an online knowledge platform on human proteins, participates in such link exchange. neXtprot entries often have associated functional gene annotations, known as geneRIFs. neXtprot users can now navigate from a neXtprot record directly to the relevant gene function statement found in the literature. Such location information can be used to reciprocally link from the annotation to the relevant sentence of the article in Europe PMC via a link-back mechanism. neXtprot, an online knowledge platform on human proteins, participates in such link exchange. neXtprot entries often have associated functional gene annotations, known as geneRIFs. neXtprot users can now navigate from a neXtprot record directly to the relevant gene function statement found in the literature.


Our aim is to make text-mining advances widely available for the benefit of the research community and we would not be able to do it without the support of our collaborators and annotation providers. Several text-mining groups have already made their annotations public in Europe PMC using the new submission system. Interested parties can share their results via Europe PMC platform, given that they adhere to the ground rules. If you would like to submit annotations please get in touch via annotations@europepmc.org. For more details join our free Annotation Submission Webinar on July 9th, 2PM GMT.

Wednesday, 1 May 2019

Making science open with the new Europe PMC plus

We are delighted to announce the launch of the new Europe PMC Plus - the manuscript submission system for authors supported by Europe PMC funders.
Europe PMC is the repository of choice for 29 international life sciences funders, who recommend or require that publications arising from the research they fund, are made openly available via Europe PMC. Grantees of Europe PMC funders can deposit their manuscripts for inclusion in Europe PMC and PMC USA using the Europe PMC plus submission system.
The new version of Europe PMC plus released on 1st May 2019 has been designed to simplify and streamline the submission process. All that’s needed to complete a submission to Europe PMC plus are citation details, submission files, and funding information. The funding is linked to the publication via an open GRIST database that contains public grant award data from all Europe PMC funders.
The submission process itself is very straightforward and is possible to complete within 10 minutes. In the best case scenario, if a manuscript is submitted correctly, and is reviewed promptly by the author, the manuscript can be made available in Europe PMC in as little as two weeks.
After announcing the start of this project just under a year ago, the new system has been developed as an open source application in partnership with the Collaborative Knowledge Foundation (Coko), eLife, Hindawi, and other community partners.
To learn how to use the new Europe PMC plus, and see what a submission process looks like, please visit our Youtube channel featuring short tutorial videos.

Monday, 25 March 2019

Prepare for the new Europe PMC plus

Europe PMC is getting ready to release an upgraded version of Europe PMC plus, a system for PIs supported by Europe PMC funders to submit accepted manuscripts for inclusion in Europe PMC and PMC. The new version of Europe PMC plus has an improved design, and new features for creating and reviewing manuscript submissions.

The new Europe PMC plus will be released on 1 May 2019. Just three things are needed to complete a submission to Europe PMC plus:

1
Citation details
Manuscripts submitted to Europe PMC plus must be accepted for publication by a peer reviewed journal. At least the article title and journal name are required.
2
Submission files
The manuscript and all related figures, tables, and supplementary materials should be uploaded to Europe PMC plus, and previewed using new tools.
3
Funding information
Researchers submitting manuscripts to Europe PMC plus must be funded by one of the Europe PMC funders. Grant information can be linked to manuscripts through a new simple search.

After a manuscript is submitted to Europe PMC plus, the submission goes through quality assurance before being processed into XML, HTML, and PDF versions for archiving, indexing, and display in Europe PMC and PMC. Before being made publicly available on Europe PMC, these web versions are made available to the reviewing researcher for a final review, to make any needed corrections.

The new submission system offers an updated design, clearer workflows, and new features, including an improved preview of submitted files, the ability to view submitted files and processed web versions side by side, and improved communication tools, which simplify creating and reviewing manuscript submissions.


My manuscripts list

Creating a submission

Checking submission input

Reviewing web versions

Since supporting open science is an important part of Europe PMC’s mission,  the new Europe PMC plus is a fully open source application. It is based on PubSweet, a free, open-source framework for building state-of-the-art publishing platforms, designed to be modular and flexible, so that individual components can be easily reused and adapted for various workflows.

The new Europe PMC plus has been developed in collaboration with the Collaborative Knowledge Foundation (Coko) and community partners including eLife and Hindawi. PubSweet community members subscribe to a common vision of creating open technologies that improve the speed of research.


To find out more about Europe PMC’s partnership with Coko to develop a web-based, open-source content and workflow management platform for manuscript ingest and processing, see http://blog.europepmc.org/2018/05/europe-pmc-and-coko-announce-partnership.html.

For more information about the other platforms that are built on top of PubSweet, visit https://coko.foundation/all-the-platforms.

For the latest updates on Europe PMC plus and other news from Europe PMC, follow us on Twitter at @EuropePMC_news.