{"id":4178,"date":"2015-06-15T18:00:20","date_gmt":"2015-06-15T16:00:20","guid":{"rendered":"http:\/\/news.embl.de\/?p=4178"},"modified":"2023-03-08T10:33:07","modified_gmt":"2023-03-08T09:33:07","slug":"1506-open-access","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/lab-matters\/1506-open-access\/","title":{"rendered":"Open access: transforming science"},"content":{"rendered":"\n

EMBL scientists are funded by the public to produce top-notch research and the organisation\u2019s open access policy makes the resulting publications freely available to everyone to read. Furthermore, a Creative Commons with attribution (CC-BY) open-access licence enables innovation in text analytics and text mining, which will be vital to enable researchers to discover relevant content efficiently in an increasingly interdisciplinary environment.<\/p>\n\n\n\n

\n

Having research outputs accessible without barrier \u2013 and properly attributed \u2013 is essential.<\/p>\n<\/blockquote>\n\n\n\n

\u201cRecognition for influential work is part of the social fabric of science,\u201d explains McEntyre. \u201cScientists, institutes and funders all want to be acknowledged when they have played a role, so having research outputs accessible without barrier \u2013 and properly attributed \u2013 is essential. But the open-access policy is about much more than that \u2013 it also encourages people to make their research reusable, so it can be explored and re-analysed in different contexts as new methods and technologies come online.\u201d<\/p>\n\n\n\n

EMBL-EBI runs Europe PMC<\/a>, a publicly accessible literature resource that holds over three million full-text articles from peer-reviewed journals and 30 million abstracts from PubMed, PubMed Central, Agricola, patent offices and many other sources. All the articles in Europe PMC can be searched in full and read freely by anyone in the world. They are also discoverable via major search engines.<\/p>\n\n\n\n

\u201cWhy should we remain stuck in this mind set, thinking that we\u2019ll all get around to reading every paper?\u201d posits McEntyre. \u201cWe all need to discover things from the literature \u2013 and that might be something big and obvious, but equally it could be just an aside in someone\u2019s paper. We need to make the whole process of exploring and consuming the scientific literature much more efficient, and text mining and analytics are a big part of that.\u201d<\/p>\n\n\n\n

\u2018CC BY\u2019 and the right to reuse<\/h3>\n\n\n\n

All of the articles in Europe PMC can be read by anyone, anywhere, any time. But open-access papers with a Creative Commons attribution license (CC-BY) or similar are much more useful, because they can be reused.<\/p>\n\n\n\n

\u201cWe make full-text articles with the appropriate licence available for download, which means that text-analytics researchers can experiment with it,\u201d says McEntyre. \u201cHaving a CC-BY license makes it possible to do computation on swathes of articles, which is fundamentally important if we\u2019re going to scour the whole of the literature for relevance and serendipitous discovery.\u201d<\/p>\n\n\n\n

\n

This is fundamentally important if we\u2019re going to scour the whole of the literature for relevance and serendipitous discovery.<\/p>\n<\/blockquote>\n\n\n\n

This becomes particularly pertinent in scientific curation work, an activity at the heart of EMBL-EBI services that involves highly skilled scientists extracting biological facts from the literature to be incorporated into various data resources. Curation adds significant value, making data easier to use, distilling knowledge about a given concept into accessible interfaces.<\/p>\n\n\n\n

Text analytics that operate on large collections of articles like Europe PMC could help improve curator activities \u2013 giving them the time and flexibility they need to focus on the trickier aspects of curation that only humans can do.<\/p>\n\n\n\n

How do people use text mining with Europe PMC? One example is the Protein Data Bank in Europe (PDBe)<\/a>, a public data resource that helps people study protein structures. Recently, PDBe started to include figures and captions from Europe PMC articles, providing much-need context for structural data records. This gives researchers a rich, multi-dimensional view of complex information, saving time and improving understanding.<\/p>\n\n\n\n

\u201cFrom the Europe PMC perspective, open access is not only about articles being free to read, but also about making the outputs of science more discoverable by linking the article narrative to related information,\u201d explains McEntyre. \u201cFor example, data presented in figures can be linked to other core public data resources, or to other sources like spreadsheets and raw images. Things like this really add value and make the literature more useful over the longer term.\u201d<\/p>\n\n\n\n

How EMBL\u2019s open-access policy works<\/h3>\n\n\n\n

A healthy percentage of Europe\u2019s life-science researchers cycle through EMBL at some point in their career, whether it\u2019s to run a research group or simply to work on a project as a visiting scientist. EMBL scientists conduct their research independently, and are free to choose which journals are best for publishing their work.<\/p>\n\n\n\n

The open-access policy does not restrict publication decisions, but does require that at minimum, wherever the work is published, the results should be made available in Europe PMC within six months of publication.<\/p>\n\n\n\n

\u201cMost journals have open-access tracks and will also deposit the \u2018final author version\u2019 on behalf of the researcher on PubMedCentral or Europe PMC,\u201d says Tobias Sack, head librarian in EMBL\u2019s Szil\u00e1rd Library. \u201cWe\u2019ve made arrangements with publishers, including Elsevier, Wiley and MacMillan, to make sure that EMBL-supported work is published open-access. They\u2019re happy to support it and in principle they support pushing the content directly to Europe PMC on EMBL\u2019s behalf.\u201d<\/p>\n\n\n\n

The Szil\u00e1rd Library at EMBL Heidelberg is on hand to help researchers with any question concerning the policy or depositing articles on Europe PMC in the event that the service is not available through the publisher. Detailed information about the open access scheme can be found on the Library\u2019s webpage<\/a>.<\/p>\n\n\n\n

Open Access and the greater good<\/h3>\n\n\n\n

EMBL\u2019s open access policy is a commitment to the public good. It makes science more open, scalable and sustainable, pooling an extremely diverse mix of results from thousands of journals covering every life-science speciality. EMBL was one of the first signatories of the H<\/em>ague Declaration<\/em> on Knowledge Discovery in the Digital Age<\/em>, which promotes ethical research practice, legislative reform and the development of open access policies and infrastructure.<\/p>\n\n\n\n

Open access has been embraced by many of the world\u2019s major science funders, some of which make funding conditional on the publication of results under open-access licenses. To make this requirement widely visible, many of Europe PMC\u2019s 28 funders \u2013 including the European Research Council, the World Health Organisation and the Biotechnology and Biological Sciences Research Council \u2013 link grant information to articles to make it easier for anyone to see the links between funding and results. By running Europe PMC, together with the University of Manchester and the British Library, EMBL bolsters the open-access movement in ways that go beyond a single institutional policy.<\/p>\n\n\n\n

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We have an obligation to address both of these barriers \u2013 not just EMBL, but the global scientific community.<\/p>\n<\/blockquote>\n\n\n\n

\u201cMany of the Intellectual Property laws around scientific publishing were established well before the web and certainly before bioinformatics came on the scene,\u201d explains Iain Mattaj, Director General of EMBL. \u201cIn many countries these laws create a barrier to analysis, although this has changed in the UK and is beginning to change across the EU as a whole. It really is a moral issue when a huge proportion of the world\u2019s scientists can simply not access new research at all. We have an obligation to address both of these barriers \u2013 not just EMBL, but the global scientific community.\u201d<\/p>\n\n\n\n

– Ends –<\/p>\n\n\n\n

This post was originally published on EMBL-EBI News<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

EMBL\u2019s new open access policy aims to make EMBL research widely and freely accessible.<\/p>\n","protected":false},"author":13,"featured_media":4242,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[3],"tags":[36,428,24,37,53,43,331,446,74,556,1317,14001,514,356],"embl_taxonomy":[],"class_list":["post-4178","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-lab-matters","tag-embl-ebi","tag-europepmc","tag-governance","tag-grenoble","tag-hamburg","tag-heidelberg","tag-mattaj","tag-mcentyre","tag-monterotondo","tag-open-access","tag-open-science","tag-osim","tag-rome","tag-szilard-library"],"acf":{"article_intro":"

EMBL\u2019s open access policy aims to make EMBL research widely and freely accessible. By ensuring that articles are published with a CC-BY licence, EMBL will make its research available not only for reading but for reuse, providing opportunities to enrich the scientific literature in ways that can transform the life and health sciences. Jo McEntyre<\/a>, head of literature services at EMBL-EBI, explains how.<\/p>\n","related_links":[{"link_description":"","link_url":""},{"link_description":"","link_url":""},{"link_description":"","link_url":""}],"article_sources":false,"vf_locked":false,"featured":false,"color":"#007B53","show_featured_image":false,"field_target_display":"","source_article":false,"in_this_article":false,"press_contact":"None","field_article_language":{"value":"english","label":"English"},"article_translations":false,"languages":""},"embl_taxonomy_terms":[],"yoast_head":"\nOpen access: transforming science | EMBL<\/title>\n<meta name=\"description\" content=\"EMBL\u2019s new open access policy aims to make EMBL research widely and freely accessible.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/lab-matters\/1506-open-access\/\" \/>\n<meta property=\"og:locale\" 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