An introduction to open science, why it's important and how to do it. This presentation was given at the European Medical Students Association (EMSA) event, 'Open Access in Action' in Berlin on 14th-15th September 2015
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.
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 software 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.
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 extrapolated 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.
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
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.
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.
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).
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
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
Open science and its advocacy
Open science and its advocacy
Digital Curation Centre, University of Glasgow
European Medical Students Association, Berlin, 14-15 September 2015 http://emsa-europe.eu/6315
Outline of the session
• Introduction to open science
• Why be open?
• How to make your publications and data open
• Questions and discussion
WHAT IS OPEN SCIENCE?
Some definitions and clarifications
Image CC-BY-NC-SA by Tom Magllery www.flickr.com/photos/lwr/13442910354
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 Information Network, Open Science case studies
More than open access publishing
CC-BY Andreas Neuhold
Why open access?
Open Access Explained!
Open access to publications
• 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
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
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”
• 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.”
Reliance on specialist research software
Slide from Neil Chue-Hong, Software Sustainability Institute
Do you use research
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
71% Have no formal
Openness at every stage
Open science image CC BY-SA 3.0 by Greg Emmerich www.flickr.com/photos/gemmerich/6365692655
and release more
Papers + Data +
Methods + Code…
Degrees of openness
Open Restricted 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
WHY PRACTICE OPEN SCIENCE?
Benefits and drivers
Image CC-BY-NC-SA by wonderwebby www.flickr.com/photos/wonderwebby/2723279491
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.
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
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)
Cut down on academic fraud
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
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.”
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
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
Get 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
Increased use and economic 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
• 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
The case of NASA Landsat satellite imagery of the Earth’s surface:
“The European Commission’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.”
But there are also opportunity costs
By Emilio Bruna
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
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”
HOW TO PRACTICE OPEN SCIENCE?
Questions to consider
Image CC-BY-NC-SA by Leo Reynolds www.flickr.com/photos/lwr/13442910354
Conduct science in the open
• Use open lab notebooks
• Share protocols
• Blog about your work
• Publish assertions to get
ideas out sooner
Routes to open access publication
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
Self-archive in a
on publisher policy.
Immediate or delayed
open access, depending
on publisher’s policy.
Search for a repository
GREEN OA ROUTE
Publish in a
Publish in an
Check SHERPA RoMEO
to see what OA and self-
archiving options are
Deposit in your local 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)
• Check OpenDOAR for examples -
Open Access Infrastructure for 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
Open access button
The Open Access Button helps you get the research you
want right now (without paying for it), and adds papers
you still need to your wishlist.
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…
Licensing research data openly
This DCC guide outlines the pros and cons
of each approach and gives practical
advice on how to implement your licence
CREATIVE COMMONS LIMITATIONS
What counts as commercial?
SA Share Alike
ND No Derivatives
Severely restricts use
These clauses are not open licenses
Horizon 2020 Open Access
guidelines point to:
EUDAT licensing tool
Answer questions to determine which licence(s) are
appropriate to use
Metadata standards to use
Use relevant standards for interoperability
Choosing appropriate file formats
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
Media Container: MP4, Ogg
Codec: Theora, Dirac, FLAC
Images TIFF, JPEG2000, PNG GIF, JPG
Structured data XML, RDF RDBMS
• Does your 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?
• OpenAIRE-CERN joint effort
• Multidisciplinary repository
• Multiple data types
– Long tail of research data
• Citable data (DOI)
• Links funding, publications,
data & software
Citing research data: why?
How to cite data
Key citation elements
• Publication date
• Location (= identifier)
• Funder (if applicable)
Plan for openness from 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
Thanks – any questions
• DCC resources on Research Data Management
• FOSTER materials on Open Science
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