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.