Open science and its advocacy
Sarah Jones
Digital Curation Centre, University of Glasgow
sarah.jones@glasgow.ac.uk
Twitter: @sjDCC
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 process.”
Research Information Network, Open Science case studies
www.rin.ac.uk/our-work/data-management-and-curation/
open-science-case-studies
More than open access publishing
CC-BY Andreas Neuhold
https://commons.wikimedia.org/wiki/File:Open_Science_-_Prinzipien.png
Why open access?
Open Access Explained!
www.youtube.com/watch?v=L5rVH1KGBCY
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
– www.sherpa.ac.uk/romeo
Open data
 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”
http://opendefinition.org
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
Reliance on specialist research 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
Openness at every stage
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
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
Under embargo
WHY PRACTICE OPEN SCIENCE?
Benefits and drivers
Image CC-BY-NC-SA by wonderwebby www.flickr.com/photos/wonderwebby/2723279491
It’s part of good research practice
Science as an open 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.
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) 
http://eprints.ecs.soton.ac.uk/22603
Cut down on academic fraud
www.nature.com/news/2011/111101/full/479015a.html
Validation of results
www.guardian.co.uk/politics/2013/apr/18/uncovered-error-george-osborne-austerity
“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.”
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
More scientific breakthroughs
www.nytimes.com/2010/08/13/health/research/13alzheimer.html?pagewanted=all&_r=0
“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
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
Funder imperatives...
“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.”
http://ec.europa.eu/research/participants/data/ 
ref/h2020/grants_manual/hi/oa_pilot/h2020-hi-
oa-pilot-guide_en.pdf
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
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 
(nanopublication)
http://openwetware.org
Collaborate & share: MyExperiment
www.myexperiment.org/workflows/16.html
Routes to open access 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
Sherpah RoMEO
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) 
http://zenodo.org
• Check OpenDOAR for examples -
http://www.opendoar.org
OpenAIRE
http://vimeo.com/108790101
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
www.openaire.eu
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.
https://openaccessbutton.org
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
www.dcc.ac.uk/resources/how-guides/license-research-data
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
NC Non-Commercial
What counts as commercial?
SA Share Alike
Reduces interoperability
ND No Derivatives
Severely restricts use
These clauses are not open licenses
Horizon 2020 Open Access 
guidelines point to:
or 
EUDAT licensing tool
Answer questions to determine which licence(s) are 
appropriate to use
http://ufal.github.io/lindat-license-selector
Metadata standards to use
Use relevant standards for interoperability
www.dcc.ac.uk/resources/metadata-standards
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
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
Data repositories
http://databib.org 
http://service.re3data.org/search
• 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?
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
Citing research data: why?
http://ands.org.au/cite-data
How to cite data
www.dcc.ac.uk/resources/briefing-papers/introduction-
curation/data-citation-and-linking
Key citation elements
• Author
• Publication date
• Title
• 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 
commercial partners
Thanks – any questions
•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