Open Science
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This document provides an overview of open science and how to practice open science. It defines open science as research carried out and communicated in a way that allows others to contribute and collaborate. The benefits of open science include increased visibility, citations, and economic benefits when data is freely available. It recommends publishing papers through open access routes, sharing data and code openly with permissive licenses, and depositing outputs in repositories to practice open science. The document provides guidance on choosing file formats, metadata standards, and repositories to openly share research outputs.
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Open Science
- 1. Open Science Sarah Jones DigitalCuration Centre, University of Glasgow [email protected] Twitter: @sjDCC Open Science – Open Data? A FOSTER/CESSDA-research data management training event, Wednesday 25th November, University of Southern Denmark
- 2. Outline of thesession • Introduction to open science • Why be open? • How to make your publications and data open • Questions and discussion
- 3. WHAT IS OPENSCIENCE? Some definitions and clarifications Image CC-BY-NC-SA by Tom Magllery www.flickr.com/photos/lwr/13442910354
- 4. What is openscience? “science carried out and communicated in a manner which allows others to contribute, collaborate and add to the research effort, with all kinds of data, results and protocols made freely available at different stages of the research process.” Research Information Network, Open Science case studies www.rin.ac.uk/our-work/data-management-and-curation/ open-science-case-studies
- 5. More than openaccess publishing CC-BY Andreas Neuhold https://commons.wikimedia.org/wiki/File:Open_Science_-_Prinzipien.png
- 6. Why open access? OpenAccess Explained! www.youtube.com/watch?v=L5rVH1KGBCY
- 7. Open access topublications • Free, immediate, online access to the results of research • Free to reuse e.g. to build tools to mine the content • Two routes to make sure anyone can access your papers – Gold route: paying APCs to ensure publishers makes copy open – Green route: self-archiving Open Access copy in repository • Find out what your publisher allows on SHERPA RoMEO – www.sherpa.ac.uk/romeo
- 8. Open data make yourstuff available on the Web (whatever format) under an open licence make it available as structured data (e.g. Excel instead of a scan of a table) use non-proprietary formats (e.g. CSV instead of Excel) use URIs to denote things, so that people can point at your stuff link your data to other data to provide context Tim Berners-Lee’s proposal for five star open data - http://5stardata.info “Open data and content can be freely used, modified and shared by anyone for any purpose” http://opendefinition.org
- 9. Open methods • Documentingand sharing workflows and methods • Sharing code and tools to allow others to reproduce work • Using web based tools to facilitate collaboration and interaction from the outside world • Open netbook science – “when there is a URL to a laboratory notebook that is freely available and indexed on common search engines.” http://drexel-coas-elearning.blogspot.co.uk/2006/09/open-notebook-science.html
- 10. Reliance on specialistresearch software Slide from Neil Chue-Hong, Software Sustainability Institute Do you use research software? What would happen to your research without software Survey of researchers from 15 UK Russell Group universities conducted by SSI between August - October 2014. DOI: 10.5281/zenodo.14809 56% Develop their own software 71% Have no formal software training
- 11. Openness at everystage Design Experiment AnalysisPublication Release Open science image CC BY-SA 3.0 by Greg Emmerich www.flickr.com/photos/gemmerich/6365692655 Change the typical lifecycle Publish earlier and release more Papers + Data + Methods + Code… Support reproducibility
- 12. Degrees of openness OpenRestricted Closed Content that can be freely used, modified and shared by anyone for any purpose Limits on who can use the data, how or for what purpose - Charges for use - Data sharing agreements - Restrictive licences - Peer-to-peer exchange - … Five star open data Unable to share Under embargo
- 13. WHY PRACTICE OPENSCIENCE? Benefits and drivers Image CC-BY-NC-SA by wonderwebby www.flickr.com/photos/wonderwebby/2723279491
- 14. It’s part ofgood research practice
- 15. Science as anopen enterprise https://royalsociety.org/policy/projects/science-public-enterprise/Report “Much of the remarkable growth of scientific understanding in recent centuries is due to open practices; open communication and deliberation sit at the heart of scientific practice.” Royal Society report calls for ‘intelligent openness’ whereby data are accessible, intelligible, assessable and usable.
- 16. Some benefits ofopenness • You can access relevant literature – not behind pay walls • Ensures research is transparent and reproducible • Increased visibility, usage and impact of your work • New collaborations and research partnerships • Ensure long-term access to your outputs • Help increase the efficiency of research
- 17. More scientific breakthroughs www.nytimes.com/2010/08/13/health/research/13alzheimer.html?pagewanted=all&_r=0 “Itwas unbelievable. Its not science the way most of us have practiced in our careers. But we all realised that we would never get biomarkers unless all of us parked our egos and intellectual property noses outside the door and agreed that all of our data would be public immediately.” Dr John Trojanowski, University of Pennsylvania
- 18. Get a citationadvantage A study that analysed the citation counts of 10,555 papers on gene expression studies that created microarray data, showed: “studies that made data available in a public repository received 9% more citations than similar studies for which the data was not made available” Data reuse and the open data citation advantage, Piwowar, H. & Vision, T. https://peerj.com/articles/175
- 19. Increased use andeconomic benefit Up to 2008 • Sold through the US Geological Survey for US$600 per scene • Sales of 19,000 scenes per year • Annual revenue of $11.4 million Since 2009 • Freely available over the internet • Google Earth now uses the images • Transmission of 2,100,000 scenes per year. • Estimated to have created value for the environmental management industry of $935 million, with direct benefit of more than $100 million per year to the US economy • Has stimulated the development of applications from a large number of companies worldwide The case of NASA Landsat satellite imagery of the Earth’s surface: http://earthobservatory.nasa.gov/IOTD/view.php?id=83394&src=ve
- 20. Funder imperatives... “The EuropeanCommission’s vision is that information already paid for by the public purse should not be paid for again each time it is accessed or used, and that it should benefit European companies and citizens to the full.” http://ec.europa.eu/research/participants/data/ ref/h2020/grants_manual/hi/oa_pilot/h2020-hi- oa-pilot-guide_en.pdf
- 21. Open Science inHorizon 2020 Peer-reviewed publications • Mandated to deposit machine- readable electronic copy of paper in repository by the date of publication • Ensure OA via green/gold routes • Embargo of 6 months (STEM) or 12 months (HSS) allowed • Bibliographic metadata must be made openly available • Aim to deposit research data Research data • Pilot for projects in named areas. Other can participate voluntarily. • Applies to research data underlying publications, plus any other data as decided by project. • Participants must: – Write a DMP as a project deliverable – Deposit data in a repository – Make it possible for others to access, mine, exploit and reuse the data – Share information on the tools needed “As open as possible, as closed as necessary ”
- 22. HOW TO PRACTICEOPEN SCIENCE? Making your publications and data open Image CC-BY-NC-SA by Leo Reynolds www.flickr.com/photos/lwr/13442910354
- 23. Routes to openaccess publication Immediate open access (via publisher) Pay Article Processing Charge (APC) - if required GOLD OA ROUTE IF OPTION EXISTS e.g. a ‘hybrid’ journal (a subscription-based journal that has a paid open access option) Immediate open access (via publisher) Pay Article Processing Charge (APC) Self-archive in a repository, based on publisher policy. Immediate or delayed open access, depending on publisher’s policy. Search for a repository http://opendoar.org GREEN OA ROUTE Publish in a subscription- based journal Publish in an open access journal Researcher decides where to publish Check SHERPA RoMEO to see what OA and self- archiving options are available www.sherpa.ac.uk/romeo
- 24.
- 25. Deposit in yourlocal repository! • Speak to the library and deposit in your IR • Consider other relevant repositories for your field too e.g. Arxiv - http://arxiv.org • Deposit in Zenodo (catch-all repository) http://zenodo.org • Check OpenDOAR for examples - http://www.opendoar.org
- 26. OpenAIRE http://vimeo.com/108790101 Open Access Infrastructurefor research in Europe • aggregates data on OA publications • mines & enriches it content by linking thing together • provides services & APIs e.g. to generate publication lists www.openaire.eu
- 27. Open access button TheOpen Access Button helps you get the research you want right now (without paying for it), and adds papers you still need to your wishlist. https://openaccessbutton.org
- 28. How to makedata open? 1. Choose your dataset(s) - What can you may open? You may need to revisit this step if you encounter problems later. 2. Apply an open license - Determine what IP exists. Apply a suitable licence e.g. CC-BY 3. Make the data available - Provide the data in a suitable format. Use repositories. 4. Make it discoverable - Post on the web, register in catalogues… https://okfn.org
- 29. www.dcc.ac.uk/resources/how-guides/license-research-data Licensing research dataopenly This DCC guide outlines the pros and cons of each approach and gives practical advice on how to implement your licence CREATIVE COMMONS LIMITATIONS NC Non-Commercial What counts as commercial? ND No Derivatives Severely restricts use These clauses are not open licenses Horizon 2020 Open Access guidelines point to: or
- 30. EUDAT licensing tool Answerquestions to determine which licence(s) are appropriate to use http://ufal.github.io/lindat-license-selector
- 31. Metadata standards touse Use relevant standards for interoperability www.dcc.ac.uk/resources/metadata-standards
- 32. Choosing appropriate fileformats If you want your data to be re-used and sustainable in the long-term, you typically want to opt for open, non-proprietary formats. Type Recommended Avoid for data sharing Tabular data CSV, TSV, SPSS portable Excel Text Plain text, HTML, RTF PDF/A only if layout matters Word Media Container: MP4, Ogg Codec: Theora, Dirac, FLAC Quicktime H264 Images TIFF, JPEG2000, PNG GIF, JPG Structured data XML, RDF RDBMS Further examples: www.data-archive.ac.uk/create-manage/format/formats-table
- 33. Data repositories http://databib.org http://service.re3data.org/search • Doesyour publisher or funder suggest a repository? • Are there data centres or community databases for your discipline? • Does your university offer support for long-term preservation? Zenodo • OpenAIRE-CERN joint effort • Multidisciplinary repository • Multiple data types – Publications – Long tail of research data • Citable data (DOI) • Links funding, publications, data & software www.zenodo.org
- 34. Plan for opennessfrom the outset Many decisions taken early on in the project will affect whether the data can be made openly available • Think about where you want to publish and include APCs in grant applications if needed • Ensure consent agreements also include permission to archive and share data for reuse by others • Seek permissions for more than just the primary project purpose if signing licences to reuse third-party data. Derivative data may not be able to be shared if it includes somebody else’s IP • Explore the potential for openness when drafting agreements with commercial partners
- 35. Thanks – anyquestions • DCC resources on Research Data Management www.dcc.ac.uk/resources • FOSTER materials on Open Science www.fosteropenscience.eu Follow us on Twitter: @fosterscience #fosteropenscience
Editor's Notes
- #7 Journal prices have outpaced inflation by more than 250% over the past 30 years 15 entire disciplines where the average price for one journal for one year is over £1000 (chemistry £4227, physics £3229). Journal called tetrahedron that’s over £40,000 Irrational to think that scientists are paid by government to do research and then the papers are locked away behind paywalls. Journals don’t do the research, employ the people or pay the reviewers.
- #11 In the last four years, we have investigated and understood the challenges of the UK research community. Anecdotally, we had a lot of evidence for people working in this area that researchers relied on software, but there had been no studies conducted. So we did this ourselves. Two areas of interest, do you use software and possibly more important, what would happen to your research without software – this is 170,000 researchers in the UK who could not conduct their research without software. This is more than just a reliance on Word or web browsers – specialist software is written into the research workflows of people from psychology to physics, from the life sciences to literature. The reliance isn’t confined to the “traditionally” computationally intensive subjects, it’s a feature of all disciplines. This means that 140,000 researchers are relying on their own coding skills.
- #18 Certain research communities have also seen the benefit of sharing data as it speeds up the process of discovery. This article shows how researchers in the field of Alzheimer’s research have agreed as a community to share data immediately to make scientific breakthroughs.
- #19 There’s also a citation advantage for individual researchers. This study by Heather Piwowar and Todd Vision looked at 10,555 paper of gene expression studies that had shared the associated microarray data. Those studies that shared data received 9% more citations.
- #20 There’s also an economic benefit, as seen by the case of the NASA landsat satellite images. These were sold until 2008 for $600 a scene. Now they’re freely available and used by Google Earth. Previously they sold 19,000 images a year, whereas now they transmit 2.1 million. The revenue has gone up incredibly too from $11.4 million to an estimated value of $935 million with direct benefit of more than $100 million. The release has also stimulated the development of applications from companies worldwide. This case study comes from the Royal Society Report on Science as an Open Enterprise.
- #21 The background to this is about making the most of the data that has been created through publicly funded research. The guidelines speak of: Improved quality of results Greater efficiency Faster to market = faster growth Improved transparency of the scientific process
- #24 We also mentioned the importance of open access publishing, so I want to walk through the different options available. Essentially researchers may choose to publish in open access journals or traditional subscription-based journals. You can check what OA options are available by searching for your journal in the RoMEO directory. If you publish in an open access journal, an Article Processing Charge may be applied. Your article will then be made immediately available via the publisher. This is often terms ‘gold OA’ Alternatively you may choose to publish with a traditional publisher. Some subscription based journals are termed ‘hybrid journals’ as they also have a gold OA option. Essentially you pay to make your individual article freely available alongside others that remain available only to subscribers. Again, once you pay the APC, your article will be freely available to all via the publisher’s website. Another, cheaper route is to follow green OA. This essentially means that you take your copy of the paper (usually a pre-print, not the publisher’s final version) and deposit that in an OA repository. You can search for a repository via OpenDOAR, or check with your institution. There is usually a local institutional repository. Once you self-archive, your article will be freely available via the repository. This is often called delayed open access as publishers will normally impose an embargo in the region of 6-12 months so they can get money from providing access to the article first. A final point to note is that gold and green routes are not mutually exclusive. You can pay an APC and also deposit in a repository. In fact, there may be an obligation / encouragement on you to do this from your funder or uni.
- #25 This is the Sherpah RoMEO service. You can search for your journal title and then see what is allowed. In this example, the author can archive a pre-print but not the publisher’s final version, and certain restrictions apply e.g. a 6 month embargo.
- #27 OpenAIRE is also worth checking out. This is an EC-funded project to provide infrastructure for open access. They’ve recently released a short video that tells you how they can help. Essentially OpenAIRE aggregates metadata from different repositories to compile a complete list of publications and related outputs. They mine and enrich the content, de-duplicating entries and linking together publications with data, details about the project, authors, funders etc. OpenAIRE also provides a number of useful services & APIs, for example you can embed a publication list for your project in your website that is automatically updated whenever someone adds a new paper to a repository (this is harvested into OpenAIRE and pushed out to your list).
- #30 Guidance from the DCC can also help researchers to understand data licensing. This guide outlines the pros and cons of each approach e.g. the limitations of some CC options The OA guidelines under Horizon 2020 point to CC-0 or CC-BY as a straightforward and effective way to make it possible for others to mine, exploit and reproduce the data. See p11 at: http://ec.europa.eu/research/participants/data/ref/h2020/grants_manual/hi/oa_pilot/h2020-hi-oa-pilot-guide_en.pdf
- #32 To make sure their data can be understood by themselves, their community and others, researchers should create metadata and documentation. Metadata is basic descriptive information to help identify and understand the structure of the data e.g. title, author... Documentation provides the wider context. It’s useful to share the methodology / workflow, software and any information needed to understand the data e.g. explanation of abbreviations or acronyms There are lots of standards that can be used. The DCC started a catalogue of disciplinary metadata standards which is now being taken forward as an international initiative via an RDA working group