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.

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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.

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.

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.

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

Unlocking the open - Europe PMC integrates with Unpaywall

It’s always frustrating to hit a paywall when you stumble across an exciting article.

Until recently, for many of us the only legal way of getting hold of the publication was to purchase the paper in question. But that is no longer the case for millions of scientific publications thanks to Unpaywall - a free, open-source tool launched by ImpactStory - a nonprofit dedicated to making scholarly research more open, accessible, and reusable.

With Unpaywall you can find free versions of the full text research papers scattered around the internet. Unpaywall harvests legally-uploaded content from over 50,000 open data sources, including open repositories, open access and hybrid journals, as well as services like DOAJ, Crossref, and even Europe PMC.

In Europe PMC, free full text is already available for 4.6 million out of 33 million records. As for the rest, an open access copy may exist in a different repository, or reside on the publisher’s website. However, users have no way of knowing that the article they are interested in may be available elsewhere. And that happens more often than you think. According to a recent study, nearly half of all scientific articles requested by Unpaywall users are already available from one of the open sources.

We believe in the power of open science, but to unlock its true potential open content needs to be easily discovered. To help address this issue, Europe PMC has teamed up with Unpaywall to help users get open access to publications easily.

You can now see the iconic green Unpaywall logo on the full text link on the Europe PMC website whenever a free version of the paper can be found using the Unpaywall service.

Here is how we do it. If a paper is available in Europe PMC, the full text link will bring you right to it.

If, however, we do not have the free full text, we use the publication’s DOI to search for an open copy via the Unpaywall API. We then use the URL returned by the API as the full text link, which appears on the article’s abstract page, like in the following example:

Whenever possible, the link will bring you directly to the PDF version of the paper in question.

According to our estimations, this service will help users discover 2.7 million open access publications in addition to the 4.6 million free full text already available in Europe PMC.

Our goal is to build a system that helps you navigate the open content effortlessly. We hope that with this new tool many more of us in and out of academia will be able to read the research literature without any barriers.

Why every researcher should care about open citations

What happens when you cite someone’s research?

As you write a research publication you include references to the work of your fellow researchers. Once the article is published in a scientific journal the readers may view the reference list to verify cited information or perhaps discover additional studies relevant to their topic. But have you ever wondered what happens with citation data that you produce and how it is being used by others?

Once the article is accepted for publication, many journal publishers will submit the article record to Crossref in order to obtain a DOI for the paper. This record will include article metadata: author names, affiliations, article title, journal name, etc. Often the publisher will also submit the references of articles in their journals to access the Cited-By Service provided by Crossref. This citation data is not released automatically - by default the references are hidden from the public eye and can only be obtained from Crossref with specific consent from the publisher.

Why do we need citations to be open?

Open citation data can be put to a good use. It improves the discoverability of the scholarly content and helps to trace knowledge back to its sources. It allows the discovery of connections within scientific research, demonstrating how a single finding may be used by scholars in different disciplines and countries. It can reveal shared authorship or common funding. Citation data is used to calculate citation rates, and can help create new transparent indicators for research evaluation.

Setting citations free: the Initiative for Open Citations

Despite its potential, the bulk of citation data has been difficult to find and access until recently. With the launch of the Initiative for Open Citations (I4OC) on April 6th, 2017 much of the previously unavailable citation data has been liberated. The I4OC has encouraged many scholarly publishers to make the references they deposit with Crossref open. Thanks to their efforts, the share of freely available citation data in Crossref has grown from 1% to over 50% (as of February 2018).

via https://i4oc.org/

What free tools are built on open citation data?

Europe PMC hosts an extensive collection of biomedical research papers, which is supplemented by an open citation network - freely available without subscription. The citation data is mainly determined from the Europe PMC content and is further supplemented with metadata supplied by Crossref. Since the launch of the I4OC the number of citations added monthly to Europe PMC via Crossref has nearly doubled. While 7.1 million references were ingested from May to October in 2016, this number has grown to 14.9 million references for the same period in 2017. As of February 2018 the Europe PMC citation network contains 316,930,434 citation links for 12.8 million citing records - nearly 44% of the 29 million journal articles.

Citation data in Europe PMC can be accessed programmatically using the citations or references modules of the RESTful or SOAP APIs. Each module returns bibliographic information: article identifier, title, author’s list, publication year, citation counts, etc. In combination with other services within Europe PMC developers’ suite, such as the Annotations API or Grants API, it represents a powerful tool for citation analysis.

Website users can access reference lists and cited-by information for a particular article in the Citation tab.

They can also use advanced search settings to retrieve publications that have been cited a certain number of times, or to access papers co-cited together.

An important thing to mention here, is that citation information is matched to Europe PMC records based on available metadata. This means that if a citation can be confidently identified, it will appear as a publication link. Readers can thus follow the reference trail through the citation network, and find research relevant to their area.

Open citation data also enables development of the powerful discovery tools. For example, in Europe PMC it is possible to sort search results by the number of citations to find the most highly cited articles on a particular topic. Citation counts for each paper are also displayed in the results list.

The cited-by information available via the Citations tab is also represented visually in a citation graph. Readers can view citation graphs on the abstract or full text page of the publication. The graph shows how frequently a paper has been referenced over time. Hovering over individual graph points brings up the number of citations for each year.

Another Europe PMC feature built using open citation data are author profiles. An author profile provides a graphical overview of the author's academic output. It is generated automatically for every researcher with a public ORCID record and ‘claimed’ works available in Europe PMC. The profile contains a publication graph showing the number of papers for any given year and a yearly citation count. Open access articles are highlighted in blue, with a darker shade representing articles licensed for reuse.

Each individual record in the profile is also displayed in the publication list together with the already familiar citation graph based on open citations. Users can sort the list by date or times cited, to see which of the works had higher impact in terms of citations.

The number of author profiles in Europe PMC is growing constantly and currently combines information for more than 650,000 biomedical researchers and over 5 million articles. To help users easily retrieve author information we have implemented a Suggested Authors feature. For an author search that matches a researcher with ORCID, a user will see a suggested authors box at the top of their results list. It will display author information for the two most prolific researchers, including their affiliation (if available), the number of publications and the number of citations. Users can then go directly to the profile page of the author using the link provided.

Taking action

Citations stitch together the global web of scholarly knowledge. To make the most of the open citations, please support the I4OC in their bold ambition: to make all citation data freely available for reuse. Get the word out about the initiative, ask journals in which you publish or do peer review to open up their citations, and finally - use the open citations in your own research and demonstrate the value of the open scholarship.

Get the essence: introducing search snippets

Reading scientific papers can be very time consuming. So you should not waste a minute searching for the relevant literature. Thanks to the cutting-edge search technologies Europe PMC helps you find facts and evidence in research publications in a blink of an eye. Search results now display snippets - highlights from the article matching your query. For every result you can see up to two snippets, separated by an ellipsis. 



Why is it important? The search term appears in context, so you can judge whether it is a negligible mention or an essential reference. This means that when sorting results by date or citation count rather than relevance, you can easily identify articles to add to your reading list thanks to the snippets shown. Not only that, but you can also quickly navigate to the place in the text, where your keywords appear. If your search terms appear in the abstract, they will be highlighted in yellow once you open the page.



To locate the keywords found in the full text take advantage of the snippet links on the abstract page. They will take you directly to the mention, saving you time of scanning through the text.



Next step? Letting the AI to read the paper for you. Learn about advances in text-mining for biomedical discovery from our recent post. We wish you happy reading!