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.
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
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:
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.
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.
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.
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