Tuesday, 4 December 2018

Bringing PubMed Commons to Europe PMC

Scientific communication does not stop at the moment of publication. Scientific discussions in the form of post-publication peer review can provide valuable insights for published articles, bring up an alternative research perspective, or even present updates for published research. At Europe PMC it’s part of our mission to support innovation in scientific publishing, and we believe that community feedback constitutes an important part of scholarly communication process. That’s why we are proud to partner with Hypothes.is, a non-profit organisation developing open annotation tools, to display post-publication comments from PubMed Commons on articles in Europe PMC.

What is PubMed Commons?

PubMed Commons was a post-publication peer review forum for authors run by the NLM (National Library of Medicine). It has been an important venue for scientific discourse of published research literature. With PubMed Commons’ departure in February 2018, comments for over 6000 PubMed-indexed articles have been carefully preserved by Hypothes.is. Every PubMed Commons comment along with replies has been transformed into a Hypothes.is annotation, available for access and reuse.

To ensure that PubMed Commons comments can be publicly accessed and explored in appropriate context, we have exposed available comments on publication pages using an open API provided by Hypothes.is.

How can I view publication comments?

You can see the comments appear on article abstract and full text pages. The link to the comments labeled as “PubMed Commons Archive” is displayed in the right-hand menu, just below the annotations tool.

Example: link to PubMed Commons comments appears on one of the articles in Europe PMC (PMID:28322189)

All comments appear in a sidebar menu in chronological order. They are presented as “page notes” - comments on a document as a whole, in contrast to annotations that are linked to a specific word or sentence in the article.

Comments are visible publicly without an account. They are displayed in view-only mode, and there is currently no option to add new comments in Europe PMC. Only comments from PubMed Commons archive are displayed on Europe PMC website, but you can explore and add other public annotations on Europe PMC articles with open tools from Hypothes.is.

We hope that this effort will provide better visibility for scholarly commentaries as an important part of the scholarly record.

Thursday, 8 November 2018

Mapping out the path to data

Data availability statements in biomedical literature

Every research paper is a story about data. Over 2.5 million articles in Europe PMC contain data of all sorts, from microscopy images to bird song recordings. While in the past, a research paper might have deciphered a single gene sequence, modern experiments often produce gigabytes of information at once. This means that data described in a paper might be spread across several databases, creating a challenge for researchers who want to access and reuse it.

To boost reproducibility and reuse of research datasets many scientific journals have introduced a data availability statement - a distinct article section that contains guidelines on data access. The data availability statement, as the name suggests, states whether the data is available, underlines conditions for access, and includes hyperlinks to publicly archived datasets analysed or generated during the study.

In fact, to date, over 230,000 full-text publications in Europe PMC contain a dedicated data availability section, with the oldest record dating to 1980. However, it’s only in 2014 that we see a sharp increase in a number of articles that include a data statement, reaching just over a quarter of all full-text articles published in 2018 so far.

*data analysis by Michael Parkin

This increase is a very positive trend in support of research reproducibility; however, there is significant variation in how Data Availability sections are included in publications across different journals. For example, they appear in a number of different places within an article, sometimes as a stand-alone section, and sometimes as part of the Methods, Results or Discussion. Many variations in the title of the Data Availability section also hamper discoverability across multiple journals.

To improve access to scientific data reported in research papers and enable analysis of data sharing practices, Europe PMC has built search filters that enable searching for data availability statements specifically. This should enable trends analysis and research into data sharing practices, potentially providing insight into how data is shared and the downstream impact of data sharing.

The right kind of search

Granular search within article sections has been available in Europe PMC for a while. It allows you to restrict your searches to figure legends or materials and methods section to get more relevant results. You can access this feature in the Europe PMC Advanced Search by selecting the section of interest from a drop-down menu.

We have recently extended the list of full text article sections available for deep searching by adding a “Data Availability” category. It unifies all different name variants mentioned above, and can be searched using (DATA_AVAILABILITY:*) syntax. For example, if you would like to retrieve papers that have data deposited in Figshare, you could search for (DATA_AVAILABILITY:Figshare).

While the search tool developed by Europe PMC can help surface the data reported in scientific literature, it relies on the publication authors to provide sufficient information on how the data can be accessed. There is great variety in data sharing practices, from data being deposited in public community database such as the European Nucleotide Archive (ENA) or the Protein Data Bank (PDB), to data included in supplemental files, in Institutional Repositories, on websites, or being available upon request from the authors.

As an example, the share of data availability statements including the word “request” has risen dramatically in the last three years, and has reached one third of all data availability statements in 2018.

*data analysis by Michael Parkin

Getting to the data

Integrating research data and literature is an important part of the Europe PMC mission to support data discovery and reuse. We identify data DOIs and accession numbers for over 40 life science resources in abstracts and full text articles using a text-mining approach. Over 450,000 publications in Europe PMC cite 1,000,000 unique datasets.

By using the advanced search tools you can identify papers that have generated protein structures, or find articles that cite proteomics datasets. The data availability section search enables you to go a step further and map out the way to supporting data. The new data search filter is one of the latest additions to the Europe PMC tools suite for locating biological data cited in the literature, including the SciLite application powered by the Annotations API, and the Data tab powered by the Data module of the Europe PMC API.

Ready for a test drive?

We hope that this new search feature for data availability can help improve reproducibility of research results, by making it easier for scientists and data enthusiasts to track underlying data from thousands of papers, wherever it may be hosted.

It can also enable detailed analyses of research data sharing practices. We can get deeper insights into the effects of publishers’ and funders’ policies on data sharing, researchers’ preferences for discipline-specific vs generic data repositories, or variations in data citations.

Whatever the use case, give the new tool a try, play with the data, and share your thoughts. We are always keen to hear your ideas and suggestions.

Thursday, 11 October 2018

Announcing new Europe PMC Beta!

We are always listening to what our users have to say. And this week we are happy to present you a Beta version of Europe PMC with lots of improvements based on extensive user feedback.

Europe PMC Beta will be available alongside the current Europe PMC website throughout October and November. You can access it at any time using the Beta link in the header of the current site.

Over the last year we’ve been making several design changes to make Europe PMC easier to use, and we’re excited to be sharing them with you! Here is a quick overview of the major updates, which mainly apply to the two key pages: search results and the article page.

Search results page

Search results have a new layout and design. You’ll notice there are labels to identify articles which are reviews or preprints, and those that have free full text or are open access and free to reuse (as shown below). You can now apply more than one search filter at a time (the current site only allows one filter to be selected). And if you want to save the citations of several articles you can add them to your export list, then review and edit the list before exporting the citations.

Article page

Most importantly, the abstract and the full text of each article have been combined into a single page. It’s great news for readers, as you no longer need to switch between different records, and can view all relevant information on the same page.

As you scroll down the article page you can discover the full text, if available, as well as useful content. We have introduced a left-hand navigation on the article page to help you find your way around the publication and related data. The navigation links to sections on the page including Figures, Full text, Data, Impact, References, Related content, and Funding. Each section is packed with handy resources, for example the Impact section will contain not only traditional article citations and alternative metrics, but also show you if the article has been cited in Wikipedia, or curated into a life science database. The Data section will be your single go-to place for all research data associated with a study, including links to the supplemental files, as well as research data cited as accession numbers or DOIs.

Figures are perhaps one of the most essential parts of a research publication - they present scientific data and summarise major results in a visual way. We have put special emphasis on figures by displaying a figure preview directly under the abstract. It allows you to quickly scan the primary data and get an overview of the key findings. The figure preview feature is only available if the article has an open access license.

We have also added a tools menu on the right for some frequently used functions. It enables you to:

- Highlight biological terms, such as organisms or gene/protein names in the article, to skim read the text

- Get the citation, if you want to cite the article

- Open the PDF

We’ve also significantly improved the Highlight Terms (also known as the SciLite annotations) feature. When you first open the side panel using the ‘Highlight terms’ link, all the unique biological terms that have been found in the abstract or full text can be seen at a glance. It’s easy to highlight the terms individually, or alternatively to highlight all terms in a category (such as diseases), and see where they appear in the article.

All design changes on Europe PMC Beta are based on user research findings and feedback. In 2017 we asked 12 researchers to complete a diary documenting their literature searches over one week, to better understand how and why they carried out literature searches in the context of their day-to-day work. We also carried out several rounds of usability testing, to evaluate how well Europe PMC works for the people who use it. If you are curious to see it, the results of our user research are published on Figshare.

An experience map illustrating how life scientists search for research literature based on user research by the Europe PMC

UX team. https://doi.org/10.6084/m9.figshare.4789744.v1

We would love to hear your thoughts on Europe PMC Beta! Please use the Feedback button to leave your feedback, or email helpdesk@europepmc.org. If you would like to take part in future Europe PMC usability testing, to help us continue to improve the website, please contact helpdesk@europepmc.org.

We will make further improvements before any of the new designs and features are available on the current Europe PMC website, and we hope that with your help we will continue creating the best tools for literature research.

Wednesday, 11 July 2018

Preprints in Europe PMC: reducing friction for discoverability

From July 2018, the Europe PMC repository will start indexing preprints. Making preprints discoverable through Europe PMC will make the science reported in preprints more widely discoverable and support their inclusion into workflows such as grant reporting, article citing and credit and attribution. This blog post explains why we have done this, and discusses some of the opportunities and challenges that arise from this decision.

In the life sciences, peer reviewed journal articles are the global currency by which we share research results, used also, in part, in funding and career decisions. But in the past few years the use of preprints - non-peer reviewed articles, posted to preprint servers - has become increasingly popular. According to Jordan Anaya of PrePubMed, over 2300 new life sciences preprints were published in June 2018 (see Fig.1), in large part driven by the use of bioRxiv.

Figure 1. Growth in preprint uptake in the life sciences (Source: http://www.prepubmed.org).

The very widespread use of preprints for biologists has a long way to go - the rate of growth is impressive, but still, as measured against the monthly ingest of peer reviewed papers by PubMed, it represents only 2-3 % of that volume. While the use of preprints has been particularly popular in computational biology and genomics, questions remain for many researchers on the long-term benefits of preprints. In recognition both of the trending popularity and the need to better understand the effect of preprints on the publishing ecosystem, Europe PMC will now be including preprint records.

Europe PMC and preprints

From July 2018, Europe PMC will include abstracts for preprints that have a DOI and can be retrieved via Crossref metadata services. This means that about 37,000 preprints will be immediately discoverable in Europe PMC; a figure which we anticipate will grow by around 2000 preprints every month.

By restricting Crossref searches by DOI prefix, the initial preprint servers to be indexed include: bioRxiv, PeerJ Preprints, ChemRxiv, F1000Res, and the Open Research platforms powered by F1000: Gates Open Res, Wellcome Open Res, HRB Open Res, AAS Open Res, and MNI Open Res. We are using this filtering approach in order to include preprints that have screening protocols in place, and to ensure we do not inadvertently include blog posts or other types of non-peer reviewed content. You can expect to find preprints in Europe PMC within 24 hours of being sent to Crossref; links to the full text on the preprint server via the DOI are included.

To distinguish preprints from peer reviewed articles in Europe PMC, each preprint is given a PPR ID, and is clearly labelled as a preprint, both on the abstract view and the search results (see Fig. 2). When preprints have subsequently been published as peer-reviewed articles and indexed in Europe PMC¹ they are crosslinked to each other. About 14,000 preprints have so far been published in peer reviewed journals via these cross-link detection methods. All preprint content will also available in Europe PMC APIs as well as on the website.

Preprints can be claimed to ORCID iDs (indeed, in the pilot set of ~120 preprints, 77 have already been linked to ORCID iDs ) and are also included in Europe PMC routine text mining processes that identify genes/proteins, organisms, diseases, and data citations, among other key biological entities.

Making preprints discoverable in Europe PMC will make the science reported in preprints more widely discoverable and support their inclusion into workflows such as grant reporting, citing and credit and attribution.

Figure 2. Search results and abstract views in Europe PMC differentiate preprint from peer-reviewed articles.

¹We use Crossref's "is-preprint-of" field as well as a basic citation metadata check to find matching peer-reviewed papers and preprints

Europe PMC as a platform for innovation

At Europe PMC, we support the use of preprints as a means to communicate research results rapidly. But we recognise that there are open questions regarding the effects of the widespread use of preprints in particular for (non-expert) readers and informations seekers, and the effects of preprints on the current life sciences publishing ecosystem. We therefore see the additional benefit of hosting preprints from several sources in Europe PMC as providing an open platform to address some of these questions. Putting preprints in the context of peer-reviewed content will help support the analysis of, for example, the impact (positive or negative) of preprints on scholarly communications overall. Do they add to churn or alleviate churn? When is a preprint cited preferentially to a peer reviewed paper? How should versions be managed across different platforms? For example, using the smart filter to retrieve all preprints that have a linked peer-reviewed paper via the Europe PMC API, and then comparing the publication dates, it is possible to reveal the median time between preprint posting and publication (Fig. 3) at around 4-5 months.

Figure 3. Time between posting a preprint and publication of a peer-reviewed article. Data taken from bioRxiv and PeerJ Preprints, using metadata supplied to Crossref. Note that a small number of preprints appear to have been posted after a peer-reviewed paper has been published, illustrating that reusing data in different contexts can provide opportunities for improved quality control. Data analysis by Michael Parkin.

The future

Aggregating a relatively small number of preprint abstracts from several different sources has already exposed some challenges in preprint management: there is variability in the scope of metadata supplied and in the handling of versions by different preprint servers. Harmonizing on these issues will require work and collaboration; we would welcome comments on these matters.

Including full text in addition to abstracts will open further questions regarding technical robustness and publishing ecosystem dynamics. With full text, we can answer deeper and perhaps more critical questions such as the impact of peer review on the evolution of a paper, and how robustly the scientific conclusions are supported re: availability of supporting data. With full text, the community can experiment on a more granular level with peer review, accreditation/badging, data integration and so on. To explore these issues fully, preprints made available in a structured format (XML) with machine-readable (and open) licenses will greatly facilitate responsible sharing, analysis and reuse of content by different communities.

Friday, 18 May 2018

Europe PMC and Coko Announce Partnership

The Collaborative Knowledge Foundation (CoKo) and Europe PMC are excited to announce a new partnership to develop web-based, open source content and workflow management components that will enable ingest and processing of manuscripts. The system will be built on Coko’s PubSweet technology framework and will contribute to the vision of creating modern, digital-first technologies that improve the speed of research.

Europe PMC will be joining a community of publishers interested in collaborating to provide the research and scientific community better tools and platforms for the publication and broad dissemination of research. Hindawi, eLife, and UC Press are also partners in this endeavor.

Michele Smith, Product Manager for Europe PMC, says: “We're delighted to team up with CoKo and partners to build an open source deposition system for accepted manuscripts - a central part of our support for the Europe PMC funders and their open access policies. Collaborating to build this open source technology is not only a sustainable approach, but also very much aligned with our mission to make Europe PMC a platform for innovation”.

Coko builds and supports community-driven open source technology and “born open” best practices for software development. The community consists of organizations adopting or using Coko technologies, partnering open source technology builders, industry organizations, standards bodies and affiliates. While open source software is freely available to all, successful open source projects are ones with wide adoption and active community support.

Strong partnerships and open source solutions can transform research communication. We’re eager to get started. As with all our efforts, we will post updates here and throughout our channels.

Wednesday, 16 May 2018

Europe PMC and the Research Excellence Framework 2021 (REF 2021)

Several questions have come into our Helpdesk regarding how articles deposited in Europe PMC count towards the REF 2021. We thought it is worth clarifying a few of the questions that have been raised.

Does content deposited in Europe PMC count towards REF 2021?

The answer is definitely yes.

The REF 2021 policy states that:

1) To be eligible for submission to the REF 2021, authors’ final peer-reviewed manuscripts must have been deposited in an institutional or subject repository.
2) Deposited material should be discoverable, and free to read and download, for anyone with an internet connection.

Europe PMC is a subject repository for the life sciences and is open to all to read and reuse. Depositing content in Europe PMC not only satisfies REF 2021 but also the policies of the 29 Europe PMC funders.

The original REF Open Access policy stated that outputs should be deposited as soon after the point of acceptance as possible, and no later than three months after this date. From 1 April 2018, the REF 2021 Open Access policy introduced an exception. The exception states that after 1 April 2018, research outputs are now acceptable for the REF when they are deposited within three months of the earliest publication date (rather than acceptance date). So how do articles in Europe PMC comply with this policy?

Accepted Manuscripts Submitted to Europe PMC

Any manuscript funded by any one of the 29 Europe PMC funders can be deposited via the Europe PMC manuscript submission system at any point after acceptance or publication. Furthermore, we can also currently provide institutions with deposit dates for submitted articles on request, and the “first published” date for any article in Europe PMC, including all of PubMed articles, is available in the Advanced Search form:

Therefore, with the 1 April 2018 exception, Europe PMC can provide the required dates to demonstrate that submitted manuscripts are REF compliant. In addition, we are currently updating our manuscript submission system; the new version, to be released this year, will include an optional field for submitters to include acceptance and/or publication dates, as well as introduce processes that will make all these dates publicly available.

Gold Open Access Articles

The vast majority of full text content in Europe PMC is deposited by publishers, many of whom archive either full gold OA or hybrid gold OA articles with us. Journals that work with us can be browsed on the Europe PMC journals list. For example, all the PLOS journals deposit gold OA articles immediately on publication, as shown in the screenshot below from the Europe PMC journals list.

At the time of writing, Europe PMC contains about 1.7M articles with a CC-type licence.

Article Availability

Regardless of deposition route, the full text of an article may not be openly available to the public until the publisher’s embargo period has been satisfied (for Europe PMC Funders, this embargo period is a maximum of 6 months after the publication date, but it may be longer e.g. 12 months for other funders or organisations). If an article is deposited in Europe PMC via the manuscript submission system prior to this date, it is held privately until the embargo date is reached. It is up to the submitting author to provide this information in the manuscript submission form.

Working with Institutional Repositories

Europe PMC strongly supports the idea that authors should only have to deposit once to comply with funder, REF 2021 and any institutional requirement: making compliance as simple as possible will increase the efficacy of open access policies and therefore make more content freely available for others to discover, read and reuse.

To support this ideal, Europe PMC supplies content to JISC’s publications router via its open APIs, which enables articles and metadata in Europe PMC to be pushed to university repositories, as appropriate. Europe PMC is also integrated into Simplectic and Converis CRIS systems, making it easy for authors to claim papers in Europe PMC to their institutional profiles. We have developed straightforward mechanisms (the External Links service) that allow Institutional Repositories to showcase their full text content on the Europe PMC website. Finally, we recently integrated Europe PMC with unpaywall, which provides users of Europe PMC with links to open full text articles, wherever they are located.

We welcome any discussion with institutional repository managers to support their REF 2021 needs.

Thursday, 19 April 2018

Swiss National Science Foundation joins Europe PMC

We're delighted to announce that the Swiss National Science Foundation joins Europe PMC as a new funder. This brings the Europe PMC funder family to 29 members.

The Swiss National Science Foundation (SNSF) supports basic science in all academic disciplines, from history to medicine and the engineering sciences. The SNSF is Switzerland’s foremost research funding organisation and finances over 3,200 projects involving 14,800 researchers each year.

Researchers funded by the Swiss National Science Foundation 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