Benefits and practice of open science
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A open science presentation focusing on the benefits to be gained and basic practices to follow. This was given on behalf of FOSTER at the Open Science Boos(t)camp event at KU Leuven on 24th October 2014.
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Benefits and practice of open science
- 1. The benefits & practice of openness Sarah Jones Digital Curation Centre, University of Glasgow sarah.jones@glasgow.ac.uk Twitter: @sjDCC Boo(s)tcamp Open Science, KU Leuven, 24th October www.kuleuven.be/research/bootcamp
- 2. WHAT DOES IT MEAN TO BE OPEN? Image by biblioteekje CC-BY-NC-SA www.flickr.com/photos/biblioteekje/3992172265
- 3. What is open science? “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
- 4. Open methods • Documenting and 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
- 5. Open access to publications • Free, immediate, online access to the results of research • 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
- 6. Open data “Open data and content can be freely used, modified and shared by anyone for any purpose” http://opendefinition.org Tim Berners-Lee’s proposal for five star open data - http://5stardata.info make your stuff 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
- 7. Openness at every stage Design www.myexperiment.org Experiment Release Publication Analysis www.taverna.org.uk www.labtrove.org Open science image CC BY-SA 3.0 by Greg Emmerich www.flickr.com/photos/gemmerich/6365692655 impactstory.org www.datacite.org https://github.com www.sherpa.ac.uk/romeo http://openwetware.org
- 8. WHY SHOULD YOU BE OPEN? Image by wonderwebby CC-BY-NC-SA www.flickr.com/photos/wonderwebby/2723279491
- 9. It’s part of good research practice
- 10. Science as an open enterprise “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. https://royalsociety.org/policy/projects/science-public-enterprise/Report
- 11. Some benefits of openness • 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
- 12. Saving wasted time OA helps to reduce time spent finding/accessing material: “If around 60 minutes were characteristic for researchers (the average time spent trying to access the last research article they had difficulty accessing), then in the current environment the time spent dealing with research article access difficulties might be costing around DKK 540 million (EUR 72 million) per year among specialist researchers in Denmark alone.” Access to research and technical information in Denmark, Houghton, Swan & Brown (2011) http://eprints.ecs.soton.ac.uk/22603
- 13. Cut down on academic fraud www.nature.com/news/2011/111101/full/479015a.html
- 14. Validation of results “It was a mistake in a spreadsheet that could have been easily overlooked: a few rows left out of an equation to average the values in a column. The spreadsheet was used to draw the conclusion of an influential 2010 economics paper: that public debt of more than 90% of GDP slows down growth. This conclusion was later cited by the International Monetary Fund and the UK Treasury to justify programmes of austerity that have arguably led to riots, poverty and lost jobs.” www.guardian.co.uk/politics/2013/apr/18/uncovered-error-george-osborne-austerity
- 15. Acceleration of the research process “As more papers are deposited and more scientists use the repository, the time between an article being deposited and being cited has been shrinking dramatically, year upon year. This is important for research uptake and progress, because it means that in this area of research, where articles are made available at – or frequently before – publication, the research cycle is accelerating.” Open Access: Why should we have it? Alma Swan www.keyperspectives.co.uk
- 16. More scientific breakthroughs “It was 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 www.nytimes.com/2010/08/13/health/research/13alzheimer.html?pagewanted=all&_r=0
- 17. A citation advantage 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
- 18. Increased use and economic benefit The case of NASA Landsat satellite imagery of the Earth’s surface: 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 http://earthobservatory.nasa.gov/IOTD/view.php?id=83394&src=ve
- 19. But there are also opportunity costs By Emilio Bruna http://brunalab.org/blog/2014/09/04/the-opportunity- cost-of-my-openscience-was-35-hours-690 For his most recent paper: 1. Double checking the main dataset and reformatting to submit to Dryad: 5 hours 2. Creating complementary file and preparing metadata: 3 hours 3. Submission of these two files and the metadata to Dryad: 45 minutes 4. Preparing a map of the locations: 1 hour 5. Submission of map to Figshare: 15 minutes 6. Cleaning up and documenting the code, uploading it to GitHub: 25 hours 7. Cost of archiving in Dryad: US$90 8. Page Charges: $600
- 20. So what needs to change? Conclusions from Emilio Bruna: • Develop a better system of incentives from the community for archiving data and code • Teach our students how to do this NOW - it’s much easier if you develop good habits early • Minimise the actual and opportunity costs We need to stop telling people “You should” and get better at telling people “Here’s how”
- 21. HOW TO PRACTICE OPEN SCIENCE Image by Paul Downey CC-BY www.flickr.com/photos/psd/3925801816
- 22. Conducting science in the open: UsefulChem http://usefulchem.wikispaces.com/EXP284
- 23. Collaboration & sharing: MyExperiment www.myexperiment.org/workflows/16.html
- 24. Open access publication Immediate open access (via publisher) Pay Article Processing Charge (APC) - if required GOLD OA ROUTE Publish in an open access journal IF OPTION EXISTS e.g. a ‘hybrid’ journal (a subscription-based journal that has a paid open access GREEN OA ROUTE Self-archive in a repository, based on publisher policy. option) Immediate open access (via publisher) Pay Article Processing Charge (APC) Immediate or delayed open access, depending on publisher’s policy. Search for a repository http://opendoar.org Publish in a subscription-based journal Researcher decides where to publish Check SHERPA RoMEO to see what OA and self-archiving options are available www.sherpa.ac.uk/romeo
- 25. Sherpah RoMEO
- 26. Deposit in your local repository! • Speak to the library and deposit in Lirias - https://lirias.kuleuven.be • Consider other relevant repositories for your field too e.g. Arxiv - http://arxiv.org • Check OpenDOAR for examples - http://www.opendoar.org
- 27. OpenAIRE Open Access Infrastructure for research in Europe http://vimeo.com/108790101 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
- 28. How to make data 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. Licensing research data Outlines 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? SA Share Alike Reduces interoperability ND No Derivatives Severely restricts use Horizon 2020 Open Access guidelines point to: or www.dcc.ac.uk/resources/how-guides/license-research-data
- 30. Potential repositories http://service.re3data.org/search http://databib.org 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
- 31. Metadata standards Use relevant standards for interoperability www.dcc.ac.uk/resources/metadata-standards
- 32. Thanks – any questions? Follow us on Twitter: @fosterscience and #fosteropenscience FOSTER training events and materials: www.fosteropenscience.eu/events
Notas del editor
- Initially I want to consider what it means to be open
- The Research Information Network ran a series of open science case studies a few years ago to look at openness across different disciplines. These included astronomy, bioinformatics, chemistry, clinical neuroimaging, epidemiology and language technology. Through this they came up with the definition. They defined open science as … The first aspect is about conducting science in an open way to encourage others to engage with it, and also sharing the outputs at various stages. I’ll unpack this definition over the next few slides
- Part of open science is working openly – having open methods. This involves documenting workflows and procedures so others can find and reuse your methods, sharing code and tools so others can reproduce your work, and using web based tools such as blogs and wikis to facilitate collaboration and interaction with others. You may come across the terms ‘open netbook science’. This was coined by Jean-Claude Bradley. It’s about having an online labnotebook that others can find and follow.
- Open science is also about providing open access to publications. This is well-established concept now, so one you’re probably familiar with. Open access is about ensuring free, immediate, online access to the results of research. There are two main routes to ensuring open access – gold where you pay publishers to make your article freely accessible so it’s not only available to those with a subscription, and green where you self-archive a copy (usually a pre-print version) in a repository. You can see what your publisher allows via Sherpa RoMEO – search for the journal title and it will tell you if there are gold, paid-for options, or what is permitted in terms of green routes (i.e. what version can be archived and under what embargo)
- Open science is also about making data available. Open data is data that can be used, modified and shared by anyone for any purpose. So for example it can be mined, exploited, reproduced, commercialised... Data under a non-commercial license wouldn’t be open as you’re restricting how it can be used and by whom. There are different levels of openness. Making content available on the web, in any format, under an open license is open data. It’s not necessarily that reusable though. By making it available as structured data, in non-proprietary formats, using URIs and linking to other data for context, makes it much more valuable.
- So we’re talking about being open at every stage, right from designing your research to conducting experiments and analysis, publishing results and releasing the associated outputs. There are tools that can help at various stages and I’ve listed a few here. Taverna for example, help with documenting workflows, while MyExperiment is a VLE that allows you to share workflows and collaborate. LabTrove is a blogging platform that integrates with instruments so you can automatically publish documentation, and OpenWetWare is a wiki to share information, know-how, and research protocols in biology & biological engineering. GitHub is a code repository to handle versioning and allow others to collaborate / reuse code. RoMEO is a lit of journal policies, re3data.org is a list of data repositories and DataCite and Impact story help you to track the citation, reuse and impact of your work.
- In the second half of the talk I’ve focus on reasons why you should be open – specifically the benefits and rewards
- I like the quote from Ewan Birney that it was never acceptable to publish papers without making data available. If you can evidence and validate your findings, how do others know that they’re right?
- The Royal Society report ‘Science as an Open Enterprise’ makes a similar point. This emphasises that much of the growth of scientific understanding is due to open practices. Being open about your work and encouraging feedback from others is at the heart of scientific practice. The report calls for ‘intelligent openness’ – data shouldn’t just be accessible, they need to be intelligible by others so they can assess and reuse them.
- What are the benefits to openness? When publications are open, it means you can access all the relevant literature regardless of whether you have a subscription or not. Open sharing also means that research is transparant and reproducible – you can validate results By sharing you will increase your visibility and the reuse of your work, which in turn leads to more collaboration and partnerships By depositing in repositories, you also safeguard your outputs since these are properly managed services that will curate your papers and data Sharing in general also makes research more efficient – it’s quicker and new discoveries are made faster
- There was a study done in Denmark on how open access saves time. They looked at the average time wasted looking for articles that were difficult to locate or gain access to (average = 60 mins per article), and extrapoloated this up to see what it was costing the sector annually. The estimate is €72 million in Denmark alone.
- Sharing data also cuts down on academic fraud. You’ve probably come across the case of Diederik Stapel – a former professor of social psychology at Tilberg University in the Netherlands. He had literally been making up data to support his hypotheses and various headlines had been picked up by the media e.g. meat eaters are more selfish than vegetarians. Some students questioned the results and the whole story unravelled, showing this had been going on for years. What’s troubling is that this had gone unnoticed. The data weren’t made available and checked, so such a history of fraud could develop.
- The validation of results is key. This article references an inadvertent error in a economics paper by Reinhadt and Rogoff. Missing some rows out of an average gave drastically different results – what was published suggested that countries with 90% debt ratios see their economies shrink by 0.1%. Instead, it should have found that they grow by 2.2% – less than those with lower debt ratios, but not a spiralling collapse. This mistake wasn’t picked up on initially as the data hadn’t been shared. The mistake fed into government policy - the findings of this paper were used as justification for austerity measures in the UK and various other countries in the EU.
- To look at things in a more positive light, this study shows how open access publishing accelerates the research process. It looks at citations rates for articles deposited in arXiv – a preprints repository in maths, physics, astronomy, computer science etc The time lag between deposit and citation of an article has been shrinking drastically year on year. Nowadays the research cycle in High-Energy Physics (HEP) is approaching maximum efficiency as a result of the early and free availability of articles that scientists in the field can use and build upon rapidly.
- 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.
- 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.
- 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.
- It’s not all positive though – otherwise why isn’t everyone already doing this. There is a certain amount of effort and cost to open science, which this blog post by Emilio Bruna highlights. He calculated the cost of sharing his data for one paper and came to a total of 35 hours and $690. He breaks this down into the cost of preparing the dataset, creating complementary metadata and associated files, cleaning up and documenting the code (which involves a big mental leap), and the charges applied.
- He suggests what needs to change and I think this is quite pertinent for today. We need a better system of incentives so you get more tangible returns from openness – better chances on grant applications, more likelihood of promotion… This is likely to evolve during your careers. If we teach people what to do now, it will become part of your processes and be easier in the long run. The learning curve won’t be as steep. We also need to focus not on why you should be open, but how – and that’s what today’s presentations should give you.
- I mentioned earlier about conducting science in the open. UsefulChem is an example of that. It’s a wiki platform where chemists can document their experiments. It’s effectively an open labnotebook. You can see here that the researcher has shared his aims, procedures, results, conclusion and a log of activities. There is also an option to comment.
- My Experiment is like a Virtual Research Environment. You can share scientific workflows that others can comment on and reuse. You can see in the sidebar that it’s clear how the workflow is licensed and who credit should be given to if reusing. There are also a number of social media features too e.g. ratings, favourites and stats for views and downloads.
- 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.
- 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.
- Speak to your library as there is usually an institutional repository you can use. There may also be relevant repositories given your field e.g. Arxiv for maths, computing science, physics etc.
- 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).
- The final aspect to discuss is open data. The Open Knowledge Foundation suggests four simple steps. First off you need to decide what to share. Not all data can be made openly available due to commercial restrictions or sensitivities. Once you’ve decided what to share, determine what IP exists and apply a suitable licence. You should then make the data available in a suitable format so others can bulk download it. Remember that for it to be useful you want to share appropriate metadata and documentation too. Using repositories is useful to make sure your data are properly managed and preserved for the long-term. The final step is to make your data discoverable. Put it online, tell others about it and add details to various registries so it gets found.
- 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
- You should select a suitable repository. The Databib and Re3data lists can be useful for this. They allow you to search and browse by subject. Re3data also allows you to restrict the search by certificates, open access repositories and persistent identifiers.
- 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