A discussion of the way the adoption of digital laboratory notebooks will change the demands on libraries and librarian in the management of data

1. The future of experimental
data: Libraries and
Laboratory Notebooks
USTLG Meeting
Promoting the role of libraries, library services
and librarians
Jeremy Frey
16 May 2014 1

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3. Outline
• Introduction
• Open Access vs Intelligent Access to Data
• The Trove Software
• Digital Notebooks - Advantages
• Data Citation
• The Future and labs and data
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4. University of Southampton Library Resources
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5. Open Data
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6. Review Article
Laboratory notebooks in the digital era: the role of
ELNs in record keeping for chemistry and other
sciences
Colin L. Bird, Cerys Willoughby and Jeremy G. Frey
Chem. Soc. Rev., 2013,42, 8157-8175
DOI: 10.1039/C3CS60122F
This article is licensed under a Creative Commons
Attribution 3.0
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7. Data Curation in the Chemical Sciences
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http://dx.doi.org/10.3789/isqv25no3.2013.02

8. Subversive
and furtive
sharing &
exploitation of
data in virtual
space
RDF
OAI
Taxi
E-
user
Labs
Digital Repository
Data
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The future of laboratory data
Some projects need large amounts of data from the literature
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10. Intelligent Open Access to Data
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11. StructureGate
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12. THE NARRATIVE
What is the story? What is the why?
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13. Faraday’s laboratory notebooks
are also remarkable in the amount
of detail that they give about the
design and setting up of
experiments, interspersed with
comments about their outcome
and thoughts of a more
philosophical kind. All are couched
in plain language, with many vivid
phrases of delightful spontaneity….
Peter Day, ‘The Philosopher’s Tree: A Selection of Michael
Faraday’s Writings’
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14. The integrity of science as a discipline rests on the ability of
scientists to reproduce the claims of others.
While none of the organic chemistry journals go to the same
lengths as Organic Syntheses, where each procedure must be
reproduced as described in an independent laboratory before
publication, ……..
sufficient detail so that the procedures can be reproduced and
provide sufficient data to establish the structures …….
This information is necessary for the review process …… to base
their experiments on published work.Methods are as important as the data
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If only I knew exactly how
she did this experiments
I know all this supplementary
information could be useful but will
people really remember the format? Is
it worth all the hassle?I wish I could get the
numbers from this
graph - the pdf is not
much use.
I wish I had
recorded things at
the start the way I
do now…..
Typical Laboratory
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16. Archiving of data
• Experiments are often repeated
– Data stored locally on a
computer and can’t be found
– Handwriting can’t be read
– Laboratory notebooks lost or
damaged
– Correct data not recorded
first time round
http://www.ecs.soton.ac.uk/regenesis/pictures
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17. 16/05/2014 The future of laboratory data
The Trove Software
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19. BlogMyData Project - Godiva
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20. LabTrove and User defined metadata
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21. A big proportion of
our users are not
really adding
metadata!
Librarians can help
here!
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22. Figure 7. Visualization of posts as a network of resources.
Milsted AJ, Hale JR, Frey JG, Neylon C (2013) LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a
Marked Up Record of Work in a Bioscience Research Laboratory. PLoS ONE 8(7): e67460. doi:10.1371/journal.pone.0067460
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067460
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23. Electronic
Laboratory
Notebooks
ELNs
Comparison with
traditional paper
notebooks
Communication
Collaboration
Sharing
Linking
Curating
• Higher Quality Record
• Natural linking to data
and external resources
• Easier Collaboration
• Improved planning
• Improved discussions
• Efficiency gain in
production of
presentations/reports
• Change the nature of
Professor/Student
interactions
Impact on researchers
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24. DATA CITATION
Supplementary data linked to laboratory notebooks
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25. doi: 10.1098/rsta.2005.1630 Phil. Trans.
R. Soc. A 15 August 2005 vol. 363 no.
1833 2075-2095
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26. Kenji Takeda, Graeme Earl, Jeremy Frey, Simon
Keay, and Alex Wade
Enhancing research publications using Rich
Interactive Narratives Phil. Trans. R. Soc. A. 2013
371 20120090; doi:10.1098/rsta.2012.0090
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Use of Deep Zoom technique
Data covers a huge range of scale and type
New ideas for presenting to avoid overload
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27. http://royalsocietypublishing.org/content/371/1983/20120090.jnl_roysco_tab_art
Use of Deep Zoom technique
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28. Select
entries
(all)
Export as HTML “static”
copy
Zip and send to
repository
LabTrove Notebooks
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29. Chemical Biology
Paper in PLoS
• Export of the entire laboratory
notebook (LabTrove) and deposit with
FigShare.
• At 50 Mb it exceeded the upload limit
of the journal!
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30. http://ses.library.usyd.edu.au/handle/2123/10461
Example from Mat Todd
University of Sydney
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DataCite DOI

32. Open Notebook
Science
• Certainly not always the way to work!
– IPR, Commercial, long term projects, recognition
issues, etc
• But
– Makes connection much easier if the data and
processes are “Open”
– Easy to export & access of “Linked-Data”
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It is not necessary to change.
Survival is not mandatory.
W. Edwards Deming
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LabTrove Open Notebooks
Mat Todd’s Malaria Project
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34. DATA EXPLOSION
CRYSTALLOGRAPHY E-
CRYSTALS
Built on the ePrints system used at Southampton as a repository for
research outputs
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35. Unavailable Information
• Not just lots of data but why are many of the
structures unpublished so certainly
unavailable?
• The E-Crystals and E-Bank
Project looked at how to
address this issue
• Is making data available
the same as depositing
a copy with someone else?
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36. 16/05/2014 The future of laboratory data
Graph/Network provides
intuitive navigation
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37. DISSEMINATION IS PART
OF THE RESEARCH
Bringing dissemination in to the lab… use and
re-use of data… the digital research notebook
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38. Change in the whole way we design and build
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3D Printers: A radical change to the experimental section
of a paper!
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39. All I am saying is that now is the time to
develop the technology to deflect an
asteroid
We must speed up the knowledge discovery process
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40. IT as a Utility
funded under Research Council UK's Digital Economy theme
The Digital Economy vision is of the
transformational impact of digital
technologies on all aspects of life.
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41. Join the ITaaU Network+
• Web: www.itutility.ac.uk
• Mailing list: http://jiscmail.ac.uk/itutility
• Hashtag #itaaun
• Twitter: SteveITaaU
• Facebook page: http://www.facebook.com/ITutilityNetwork
• Email: info@itutility.ac.uk
• LinkedIn group: IT-as-Utility-Network
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ITaaU Network meeting 19 & 20th June
Southampton Hilton

42. Trust me Mort - no electronic communications
superhighway, no matter how vast and sophisticated,
will ever replace the art of the schmooze
Thank you for listening
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