Opening webinar for the Open Access week 2016
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CC BY-SA 4.0 OPEN DATA sharing the main actor of a scientific story pcmasuzzo 24 October 2016 paola masuzzo Extra logo Extra logo
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Transcript of Opening webinar for the Open Access week 2016
CC BY-SA 4.0
OPEN DATAsharing the main actor of a scientific story
pcmasuzzo
24 October 2016 paola masuzzo
Extra logo Extra logo
CC BY-SA 4.0
What is exactly open data?
Why should you make your data open?
How can you make your data open?
My open data story
CC BY-SA 4.0
What is exactly open data?
Why should you make your data open?
How can you make your data open?
My open data story
CC BY-SA 4.0
Open data implies freedom to access, use and re-use for any purpose
http://opendefinition.org/od/
CC BY-SA 4.0
Open data implies freedom to access, use and re-use for any purpose
http://opendefinition.org/od/; http://opendefinition.org/licenses/
There are many open knowledge definition conformant licenses
CC0 waiverhttps://creativecommons.org/publicdomain/zero/1.0/
CC BY (Attribution only)https://creativecommons.org/licenses/by/4.0/
CC BY-SA (Attribution ShareAlike)https://creativecommons.org/licenses/by-sa/4.0/
CC BY-SA 4.0
Open data implies freedom to access, use and re-use for any purpose
http://opendefinition.org/od/; http://opendefinition.org/licenses/
There are many open knowledge definition conformant licenses
CC0 waiverhttps://creativecommons.org/publicdomain/zero/1.0/
CC BY (Attribution only)https://creativecommons.org/licenses/by/4.0/
CC BY-SA (Attribution ShareAlike)https://creativecommons.org/licenses/by-sa/4.0/
CC BY-SA 4.0
What is exactly open data?
Why should you make your data open?
How can you make your data open?
My open data story
CC BY-SA 4.0
Research data need to be treated asfirst-class citizens in science
Vines et al., Current Biology, 2014; image courtesy Auke Herrema
CC BY-SA 4.0
Research data need to be treated asfirst-class citizens in science
Vines et al., Current Biology, 2014; image courtesy Auke Herrema
Data should themselves be considered the primary output
of research
CC BY-SA 4.0
One could just argue that data produced with public funds belong to the public
Image courtesy Auke Herrema
CC BY-SA 4.0
But there are so many more great reasonsfor data to be open
develop newanalysis methods
improve research practices
guarantee data preservation
reduce cost of science
engagewith citizens
increase visibility and collaborations
science-driven motivations
society-driven motivations
data usersbenefits
data producersbenefits
enhance reproducibility
ask new questions
advance science
CC BY-SA 4.0
Open data means more hands at work, more brain power and faster innovations
Gina Kolata, The New York Times, 2010; SCIENCEMAG 2016 - Williamson et al., 2016
CC BY-SA 4.0
Open data creates a culture of transparency and potentially discourages fraud
Wicherts et al., PloS one, 2011
“Willingness to share research data is related to the strength of the evidence and the quality of reporting of statistical results”
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Open data means more reproducibility and better research practices
Monya Baker, Nature, 2016; image courtesy Auke Herrema
CC BY-SA 4.0
Open data means also visibility and a higher chance to get cited
Piwowar et al., PeerJ, 2013
citationadvantage
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What is exactly open data?
Why should you make your data open?
How can you make your data open?
My open data story
CC BY-SA 4.0
The Panton Principles are a pretty good starting point
1. When publishing data, make an explicit and robust statement of your wishes.
2. Use a recognized copyright waiver or license that is appropriate for data.
3. If you want your data to be effectively used and added to by others, it should be open as defined by the Open Knowledge/Data Definition—in particular, non-commercial and other restrictive clauses should not be used.
4. Explicit dedication of data underlying published science into the public domain via PDDL (http://opendatacommons.org/licenses/pddl/1-0/) or CCZero (http://creativecommons.org/publicdomain/zero/1.0/) is strongly recommended and ensures compliance with both the Science Commons Protocol for Implementing Open Access Data and the Open Knowledge/Data Definition.
http://pantonprinciples.org
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A lot of repositories are available to upload research materials and data
CC BY-SA 4.0
A lot of repositories are available to upload research materials and data
CC BY-SA 4.0
You certainly don’t need to know more than 1,500 repositories by heart
https://biosharing.org/databases/
CC BY-SA 4.0
There also exist a number of data journals
CC BY-SA 4.0
Making data available is only one half of the open data equation
intelligent access to the data and interoperability are crucial
Wilkinson et al., 2016, Scientific Data; https://www.force11.org/group/fairgroup
CC BY-SA 4.0
What is exactly open data?
Why should you make your data open?
How can you make your data open?
My open data story
CC BY-SA 4.0
Cell migration experiments are complex and produce diverse and rich data sets
sample preparation
image acquisition
image processing
data analysis
Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0
CC BY-SA 4.0
Cell migration experiments are complex and produce diverse and rich data sets
Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0
• paper laboratory notebooks
• electronic laboratory notebooks
• spreadsheets• text files• protocols• papers...
• raw files• XML files• proprietary
microscope or acquisition software files ND2 for Nikon, LIF for Leica, OIB or OIF for Olympus, LSM or ZVI for Zeiss
• OME-TIFF
• image files with pixel values and metadata
• png, jpeg, tiff, avi• text files describing
processing algorithms
• text files describing extracted features
• graphs, plots• analysis pipelines• text files describing
computational algorithms...
sample preparation
image acquisition
image processing
data analysis
CC BY-SA 4.0
CellMissy is our open-source tool for cell migration data management and analysis
0 3h 6h
wound
cells
Experiment
Data Analyzer
Data Loader
Collective cell migration Single-cell migration
Experiment Manager
Masuzzo et al., Bioinformatics, 2013; https://github.com/compomics/cellmissy
CC BY-SA 4.0
CellMissy enables data and metadata exchange
lab A
CC BY-SA 4.0
CellMissy enables data and metadata exchange
lab A lab B
CC BY-SA 4.0
CellMissy enables data and metadata exchange
lab B
This is one file in CellMissy! (≈10 MB)
lab A
CC BY-SA 4.0
But we can easily extend this conceptto a bigger scale
DataRepository Local Software
CC BY-SA 4.0
And so we did it!
Cell migration workshop, Ghent, March 2014; Masuzzo et al., Trends in Cell Biology, 2015
CC BY-SA 4.0
An open data exchange ecosystem for cell migration research is now on its way
Masuzzo et al., Trends in Cell Biology, 2015
CC BY-SA 4.0Image courtesy Auke Herrema
CC BY-SA 4.0Image courtesy Auke Herrema
CC BY-SA 4.0
Thank you!
