USTLG Talk: The future of laboratory data: Libraries, Librarians and Digital Laboratory Notebooks
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Transcript of USTLG Talk: The future of laboratory data: Libraries, Librarians and Digital Laboratory Notebooks
The future of experimental data: Libraries and Laboratory Notebooks
USTLG Meeting
Promoting the role of libraries, library services and librarians
Jeremy Frey16 May 2014 1
16/05/2014 The future of laboratory data 2
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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University of Southampton Library Resources
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Open Data
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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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Data Curation in the Chemical Sciences
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http://dx.doi.org/10.3789/isqv25no3.2013.02
Subversive
and furtive
sharing &
exploitation of
data in virtual
space RDF
OAI Taxi
E-
user
LabsDigital Repository
Data16/05/2014
The future of laboratory data
Some projects need large amounts of data from the literature
8
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Intelligent Open Access to Data The future of laboratory data16/05/2014
10
StructureGate
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THE NARRATIVE
What is the story? What is the why?
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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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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 Laboratory15
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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16/05/2014 The future of laboratory data
The Trove Software
17
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BlogMyData Project - Godiva
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LabTrove and User defined metadata
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A big proportion of our users are not
really adding metadata!
Librarians can help here!
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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
16/05/2014 The future of laboratory data 22
ElectronicLaboratoryNotebooks
ELNs
Comparison with traditional paper
notebooks
Communication Collaboration
SharingLinking
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 researchers16/05/2014 The future of laboratory data 23
DATA CITATION
Supplementary data linked to laboratory notebooks
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doi: 10.1098/rsta.2005.1630 Phil. Trans.
R. Soc. A 15 August 2005 vol. 363 no.
1833 2075-2095
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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
26
http://royalsocietypublishing.org/content/371/1983/20120090.jnl_roysco_tab_art
Use of Deep Zoom technique
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Select
entries
(all)
Export as HTML “static”
copy
Zip and send to
repository
LabTrove Notebooks
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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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http://ses.library.usyd.edu.au/handle/2123/10461
Example from Mat Todd
University of Sydney
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DataCite DOI
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
32
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LabTrove Open Notebooks
Mat Todd’s Malaria Project
33
DATA EXPLOSIONCRYSTALLOGRAPHY E-CRYSTALS
Built on the ePrints system used at Southampton as a repository for research outputs
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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 availablethe same as depositing a copy with someone else?
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Graph/Network provides
intuitive navigation
36
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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Change in the whole way we design and build
16/05/2014 The future of laboratory data3D Printers: A radical change to the experimental section
of a paper!38
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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IT as a Utilityfunded 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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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: [email protected]
• LinkedIn group: IT-as-Utility-Network16/05/2014 The future of laboratory data 41
ITaaU Network meeting 19 & 20th June
Southampton Hilton
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
The future of laboratory data16/05/201442