Category Archives: oa.europe_pmc

Discover drug targets with Europe PMC Machine Learning Dataset and Open Targets – YouTube

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“This webinar introduces the Europe PMC human-annotated full-text corpus for Gene/Proteins, Diseases and Organisms and highlights how it has been used to train machine learning models for systematic identification and prioritisation of potential therapeutic drugs by the Open Targets Platform. This webinar will explain how to access and reuse the annotated corpus as an open community resource and provide an overview of the Open Targets Platform.

Europe PMC is an open access life science database of journal articles and preprints, containing over 41 million abstracts and 8.7 million full-text articles. Open Targets Platform is an innovative public-private partnership that uses human genetics and genomics data for systematic drug target identification and prioritisation….”

Blog – Europe PMC: Europe PMC adopts the Principles of Open Scholarly Infrastructure

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“As a long-standing service and infrastructure provider in the open science ecosystem, Europe PMC supports the Principles of Open Scholarly Infrastructure (POSI). We welcome the momentum gathering behind this initiative to promote the need to support and sustain the open infrastructure.

Europe PMC has been a part of the public and open infrastructure for over 15 years and is run and managed by EMBL-EBI (which is part of the pan-European organisation of EMBL). It is funded by 34 international funders and is community-driven, open infrastructure, set in the context of key global open data resources such as the European Nucleotide Archive (INSDC), the wwPDB and the European Genome-Phenome Archive. All of these resources exist for the public good, led by scientific need and international collaborations, and have open governance structures and a commitment to long-term sustainability. Together with PMC USA, Europe PMC is a part of the PubMed Central International archive network, which plays an integral part in fulfilling shared goals to enable international open science. Europe PMC has been selected as an ELIXIR Core Data Resource, which means that it is of fundamental importance to the wider life-science community and the long-term preservation of biological data….”

Funders – About – Europe PMC

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“Europe PMC has 33 research funders, across Europe. The Europe PMC funders expect:

Research outputs arising from research that we fund to be made freely and readily available;
Electronic copies of any biomedical research papers that have been accepted for publication in a peer-reviewed journal, and are supported in whole or in part by funding from any of the Europe PMC Funders, to be made available through PubMed Central (PMC) and Europe PMC, as soon as possible and in any event within six months of the journal publisher’s official date of final publication;
Authors and publishers, if an open access fee has been paid, to license research papers such that they may be freely copied and re-used for purposes such as text and data mining, provided that such uses are fully attributed. This is also encouraged where no fee has been paid….”

NIHR Open Access policy – articles submitted before 1 June 2022

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“DHSC and NIHR require that NIHR-funded researchers publish their main study findings in a peer-reviewed, open access journal.

Research should be published in a journal that makes the findings available using the Creative Commons Attribution (CC BY) licence, and allows immediate deposit of the final published version in other repositories without restriction on re-use. If this is not possible, then the authors must reconsider the appropriateness of the original publication and how to comply with the point above.
A copy of the final manuscript of any research papers supported in whole or in part by the NIHR should be deposited with Europe PMC upon acceptance for publication, to be made freely available as soon as possible and in any event within six months of the journal publisher’s official date of final publication.
It is expected that award holders will make provision from their funding award to cover the costs of publishing in an open access journal (previous transition arrangements have been withdrawn). If necessary, researchers may need to contact the awarding NIHR coordinating centre to discuss covering open access costs. This requirement does not apply to any recipient of NIHR funding prior to 1 April 2014, who remain under the requirements of their original contract. However, it is recommended that these award holders contact the appropriate NIHR managing centre to discuss publication.
The above should not prevent researchers from also depositing a copy in their own institutional or another subject-based repository should they choose to do so, or be required to do so by their employing institution subject to any restrictions from the publishers….”

Blog – Europe PMC: Transparency for preprints: handling withdrawals and removals

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“Part of the appeal of preprints is the ability to post new versions, allowing researchers to continuously improve their manuscript and correct it if needed. However, in some cases the data or its interpretation presented in the preprint may be proven incorrect with time. In such cases the authors may wish to withdraw or remove the preprint, rather than posting another version. There could also be instances where preprints are removed for legal reasons, due to authorship disputes, or even as a result of erroneous posting. 

Currently, there are several different ways in which preprint platforms handle such scenarios. In the case of a withdrawal the preprint itself is often still accessible, but it is supplemented with a new version containing a withdrawal notice, which explains that the preprint should not be considered part of the scientific record. This is akin to retractions for peer reviewed journal articles. On the other hand, in the case of a removal all preprint versions are removed and the content is no longer accessible, in some cases with a removal notice replacing the preprint itself. You can see the list of different withdrawal/removal policies in the ASAPbio Preprint Server Directory.

For an archive, such as Europe PMC, it is crucial to follow best practices for handling preprint metadata to enable transparency and build trust in preprints. As a proof-of-concept we now provide a way to search and display withdrawn and removed preprints with appropriate labels for the COVID-19 full text preprint subset. We identify preprint withdrawal or removal notices based on document length (notices are often just a single sentence long) using the Europe PMC plus submission system. Those records are then flagged, manually checked and tagged with the appropriate withdrawal or removal article-type [Hamelers A, Parkin M. A full text collection of COVID-19 preprints in Europe PMC using JATS XML]….”

NIHR Open Access policy – for publications submitted on or after 1 June 2022

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“Open access makes published academic research freely, immediately and permanently available online for anyone to read, share and reuse. This maximises the societal, academic, and economic impact of publicly funded research, and enhances the integrity and rigour of research through greater openness and transparency. This policy supports the Government R&D Roadmap and our commitment to adding value in research, one aspect of which is ensuring that research results are published in full in an accessible and unbiased report. Through the NIHR Journals Library and NIHR Open Research, we enable findings, including negative findings, from all NIHR funded research to be made open access.

The NIHR Open Access Policy is focused on our expectations in relation to publishing academic, peer-reviewed journal articles – but this is just one way in which our researchers may choose to disseminate their research findings. We recognise and encourage a diversity of approaches to disseminating research findings so that people can make use of them. We are also committed to making sure that when we assess research outputs during funding decisions, we consider the intrinsic merit of the work and not the journal in which it is published (see our position on responsible use of metrics).

This policy applies to peer-reviewed articles describing NIHR funded research findings submitted on or after 1 June 2022, when it will supersede the NIHR open access policy introduced in 2014. The revised open access policy follows extensive engagement with a wide range of stakeholders including the academic, publishing and health and care sectors and patients and the public. This included an open survey in autumn 2020 to inform the future of NIHR open access policy, public contributor workshops to capture the views of patients, carers, service users and the public on this agenda, a roundtable for health and social care organisations in collaboration with Health Education England, and an independent report on the challenges and opportunities of open access in Low- and Middle-Income Countries. Find out more about the Review and its supporting evidence. Key terms are explained in the glossary….

All in-scope articles must be published under the Creative Commons attribution licence (CC BY), or Open Government Licence (OGL) when subject to Crown Copyright, to ensure maximum impact. This will permit all users of NIHR-funded articles to disseminate and build upon the material for any purpose without further permission or fees being required….”

News: New Open Access policy for NIHR funded researchers | NIHR

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“The NIHR has today announced its new Open Access policy, requiring all peer-reviewed research articles arising from NIHR-funded research studies to be made immediately open access under an open licence. 

In line with the Government’s commitment to Open Access, which “requires that research outputs funded by the UK government are freely available to the taxpayer who funds research” (R&D Roadmap), this new policy will allow evidence from NIHR funded research to be freely accessed and used across the health and social care system, empower patients and the public, and drive further innovation globally.

Based on extensive engagement with stakeholders, including members of the public, and review of evidence, NIHR has developed a new policy that will ensure that NIHR funded research findings are freely accessible, discoverable and reusable to all, including through Europe PMC. This change will apply to all peer-reviewed articles submitted for publication on or after 1 June 2022….”

Preprints 101 for authors | EMBL-EBI Training

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“Preprints enable researchers to rapidly share their work publicly before the formal peer review process. In this webinar you will learn more about preprints and their benefits for the research community from ASAPbio (Accelerating Science and Publication in biology); will hear an author’s perspective on posting preprints from Sumeet Pal Singh, a group leader at IRIBHM, ULB; and will find out how to incorporate preprints in your literature search routine by using the preprint discovery tools developed by Europe PMC….”

Five stories showing how Europe PMC is used by the life sciences community – YouTube

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“Europe PMC (https://europepmc.org/?) is an open science platform that enables access to a worldwide collection of life science publications. Watch this video and see how Europe PMC helps the scientific community to complete their everyday tasks. Read more on the blog post: https://bit.ly/2QnZqNu?. …”

Blog – Europe PMC: Announcing the new version of SciLite – the Europe PMC tool for highlighting annotations

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“This month, Europe PMC released a new version of SciLite, a powerful tool for highlighting annotations in life sciences publications. SciLite is powered by the Europe PMC annotation platform via the open annotation API, which provides access to over 1.3 billion annotations. Highlighting annotations in the text enables users to easily scan the article and locate key biological entities, such as genes/proteins, accession numbers, protein interactions, diseases, gene-disease relationship and more….”

Europe PMC: unlocking the potential of COVID-19 preprints | European Bioinformatics Institute

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“Summary

Europe PMC is now indexing full-text preprints related to the COVID-19 pandemic and the SARS-CoV-2 virus, as well as the underlying data
The project will make COVID-19 scientific literature available as fast as possible in a single repository, in a format that allows text mining
Researchers and healthcare professionals will be able to access and reuse preprints more easily, accelerating research into better treatments or a vaccine….”

Blog – Europe PMC: The new Europe PMC is here

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“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….”

Announcing new Europe PMC Beta!

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“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….

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.…

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….”

Extracting research evidence from publications | EMBL-EBI Train online

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“Extracting research evidence from publications Bioinformaticians are routinely handling big data, including DNA, RNA, and protein sequence information. It’s time to treat biomedical literature as a dataset and extract valuable facts hidden in the millions of scientific papers. This webinar demonstrates how to access text-mined literature evidence using Europe PMC Annotations API. We highlight several use cases, including linking diseases with potential treatment targets, or identifying which protein structures are cited along with a gene mutation.

This webinar took place on 5 March 2018 and is for wet-lab researchers and bioinformaticians who want to access scientific literature and data programmatically. Some prior knowledge of programmatic access and common programming languages is recommended.

The webinar covers: Available data (annotation types and sources) (1:50) API operations and parameters and web service outputs (8:08) Use case examples (16:56) How to get help (24:16)

You can download the slides from this webinar here. You can learn more about Europe PMC in our Europe PMC: Quick tour and our previous webinar Europe PMC, programmatically.

For documentation, help and support visit the Europe PMC help pages or download the developer friendly web service guide. For web service related question you can get in touch via the Google group or contact the helpdesk [at] europepmc.org”>help desk.”