The future of experimental
data: Libraries and
Laboratory Notebooks
USTLG Meeting
Promoting the role of libraries, library...
16/05/2014 The future of laboratory data 2
Outline
• Introduction
• Open Access vs Intelligent Access to Data
• The Trove Software
• Digital Notebooks - Advantages
•...
University of Southampton Library Resources
16/05/2014 The future of laboratory data 4
Open Data
16/05/2014 The future of laboratory data 5
Review Article
Laboratory notebooks in the digital era: the role of
ELNs in record keeping for chemistry and other
science...
Data Curation in the Chemical Sciences
16/05/2014 The future of laboratory data 7
http://dx.doi.org/10.3789/isqv25no3.2013...
Subversive
and furtive
sharing &
exploitation of
data in virtual
space
RDF
OAI
Taxi
E-
user
Labs
Digital Repository
Data
1...
16/05/2014 The future of laboratory data 9
Intelligent Open Access to Data
The future of laboratory data16/05/2014
10
StructureGate
16/05/2014 The future of laboratory data 11
THE NARRATIVE
What is the story? What is the why?
16/05/2014 The future of laboratory data 12
Faraday’s laboratory notebooks
are also remarkable in the amount
of detail that they give about the
design and setting up ...
The integrity of science as a discipline rests on the ability of
scientists to reproduce the claims of others.
While none ...
16/05/2014 The future of laboratory data
If only I knew exactly how
she did this experiments
I know all this supplementary...
Archiving of data
• Experiments are often repeated
– Data stored locally on a
computer and can’t be found
– Handwriting ca...
16/05/2014 The future of laboratory data
The Trove Software
17
16/05/2014 The future of laboratory data 18
BlogMyData Project - Godiva
16/05/2014 The future of laboratory data 19
LabTrove and User defined metadata
16/05/2014 The future of laboratory data 20
A big proportion of
our users are not
really adding
metadata!
Librarians can help
here!
16/05/2014 The future of laborator...
Figure 7. Visualization of posts as a network of resources.
Milsted AJ, Hale JR, Frey JG, Neylon C (2013) LabTrove: A Ligh...
Electronic
Laboratory
Notebooks
ELNs
Comparison with
traditional paper
notebooks
Communication
Collaboration
Sharing
Linki...
DATA CITATION
Supplementary data linked to laboratory notebooks
16/05/2014 The future of laboratory data 24
doi: 10.1098/rsta.2005.1630 Phil. Trans.
R. Soc. A 15 August 2005 vol. 363 no.
1833 2075-2095
16/05/2014 The future of lab...
Kenji Takeda, Graeme Earl, Jeremy Frey, Simon
Keay, and Alex Wade
Enhancing research publications using Rich
Interactive N...
http://royalsocietypublishing.org/content/371/1983/20120090.jnl_roysco_tab_art
Use of Deep Zoom technique
16/05/2014 The f...
Select
entries
(all)
Export as HTML “static”
copy
Zip and send to
repository
LabTrove Notebooks
16/05/2014 The future of l...
Chemical Biology
Paper in PLoS
• Export of the entire laboratory
notebook (LabTrove) and deposit with
FigShare.
• At 50 Mb...
http://ses.library.usyd.edu.au/handle/2123/10461
Example from Mat Todd
University of Sydney
16/05/2014 The future of labor...
16/05/2014 The future of laboratory data 31
DataCite DOI
Open Notebook
Science
• Certainly not always the way to work!
– IPR, Commercial, long term projects, recognition
issues, e...
16/05/2014 The future of laboratory data
LabTrove Open Notebooks
Mat Todd’s Malaria Project
33
DATA EXPLOSION
CRYSTALLOGRAPHY E-
CRYSTALS
Built on the ePrints system used at Southampton as a repository for
research ou...
Unavailable Information
• Not just lots of data but why are many of the
structures unpublished so certainly
unavailable?
•...
16/05/2014 The future of laboratory data
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 n...
Change in the whole way we design and build
16/05/2014 The future of laboratory data
3D Printers: A radical change to the ...
All I am saying is that now is the time to
develop the technology to deflect an
asteroid
We must speed up the knowledge di...
IT as a Utility
funded under Research Council UK's Digital Economy theme
The Digital Economy vision is of the
transformati...
Join the ITaaU Network+
• Web: www.itutility.ac.uk
• Mailing list: http://jiscmail.ac.uk/itutility
• Hashtag #itaaun
• Twi...
Trust me Mort - no electronic communications
superhighway, no matter how vast and sophisticated,
will ever replace the art...
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USTLG Talk: The future of laboratory data: Libraries, Librarians and Digital Laboratory Notebooks

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

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  • a researcher-centric web- and cloud-based ELN Blogging style – and so is flexible, lets the researchers record whatever they want to
  • Comments on computational models – in this case GODIVA is a way to show ocean models over the web (University of Reading) and with LabTrove added people can comment on geo-coded regions of the models results and have the video in the post – metadata taken from the models and put in the Trove.
  • Users can define their own metadata – two types, section and key/value – these aid with navigation in the notebook as shown on the right hand side and also with search in a LabTrove instance.
  • 1/3 use only 1 section½ use a ‘catch-all’ section70% use less than 5 sections50% use no keysLess than 20% use more than 5 keys
  • Wells H.G(1937) World brain: the idea of a permanent world encyclopaedia. EncyclopédieFrançaise, Tome 18, 24-11-12..
  • Add figshare image
  • USTLG Talk: The future of laboratory data: Libraries, Librarians and Digital Laboratory Notebooks

    1. 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
    2. 2. 16/05/2014 The future of laboratory data 2
    3. 3. Outline • Introduction • Open Access vs Intelligent Access to Data • The Trove Software • Digital Notebooks - Advantages • Data Citation • The Future and labs and data 16/05/2014 The future of laboratory data 3
    4. 4. University of Southampton Library Resources 16/05/2014 The future of laboratory data 4
    5. 5. Open Data 16/05/2014 The future of laboratory data 5
    6. 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 16/05/2014 The future of laboratory data 6
    7. 7. Data Curation in the Chemical Sciences 16/05/2014 The future of laboratory data 7 http://dx.doi.org/10.3789/isqv25no3.2013.02
    8. 8. Subversive and furtive sharing & exploitation of data in virtual space RDF OAI Taxi E- user Labs Digital Repository Data 16/05/2014 The future of laboratory data Some projects need large amounts of data from the literature 8
    9. 9. 16/05/2014 The future of laboratory data 9
    10. 10. Intelligent Open Access to Data The future of laboratory data16/05/2014 10
    11. 11. StructureGate 16/05/2014 The future of laboratory data 11
    12. 12. THE NARRATIVE What is the story? What is the why? 16/05/2014 The future of laboratory data 12
    13. 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’ 16/05/2014 The future of laboratory data 13
    14. 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 16/05/2014 The future of laboratory data 14
    15. 15. 16/05/2014 The future of laboratory data 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 15
    16. 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 16/05/2014 The future of laboratory data 16
    17. 17. 16/05/2014 The future of laboratory data The Trove Software 17
    18. 18. 16/05/2014 The future of laboratory data 18
    19. 19. BlogMyData Project - Godiva 16/05/2014 The future of laboratory data 19
    20. 20. LabTrove and User defined metadata 16/05/2014 The future of laboratory data 20
    21. 21. A big proportion of our users are not really adding metadata! Librarians can help here! 16/05/2014 The future of laboratory data 21
    22. 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 16/05/2014 The future of laboratory data 22
    23. 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 16/05/2014 The future of laboratory data 23
    24. 24. DATA CITATION Supplementary data linked to laboratory notebooks 16/05/2014 The future of laboratory data 24
    25. 25. doi: 10.1098/rsta.2005.1630 Phil. Trans. R. Soc. A 15 August 2005 vol. 363 no. 1833 2075-2095 16/05/2014 The future of laboratory data 25
    26. 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 16/05/2014 The future of laboratory data Use of Deep Zoom technique Data covers a huge range of scale and type New ideas for presenting to avoid overload 26
    27. 27. http://royalsocietypublishing.org/content/371/1983/20120090.jnl_roysco_tab_art Use of Deep Zoom technique 16/05/2014 The future of laboratory data 27
    28. 28. Select entries (all) Export as HTML “static” copy Zip and send to repository LabTrove Notebooks 16/05/2014 The future of laboratory data 28
    29. 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! 16/05/2014 The future of laboratory data 29
    30. 30. http://ses.library.usyd.edu.au/handle/2123/10461 Example from Mat Todd University of Sydney 16/05/2014 The future of laboratory data 30
    31. 31. 16/05/2014 The future of laboratory data 31 DataCite DOI
    32. 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” 16/05/2014 The future of laboratory data It is not necessary to change. Survival is not mandatory. W. Edwards Deming 32
    33. 33. 16/05/2014 The future of laboratory data LabTrove Open Notebooks Mat Todd’s Malaria Project 33
    34. 34. DATA EXPLOSION CRYSTALLOGRAPHY E- CRYSTALS Built on the ePrints system used at Southampton as a repository for research outputs 16/05/2014 The future of laboratory data 34
    35. 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? 16/05/2014 The future of laboratory data 35
    36. 36. 16/05/2014 The future of laboratory data Graph/Network provides intuitive navigation 36
    37. 37. DISSEMINATION IS PART OF THE RESEARCH Bringing dissemination in to the lab… use and re-use of data… the digital research notebook 16/05/2014 The future of laboratory data 37
    38. 38. Change in the whole way we design and build 16/05/2014 The future of laboratory data 3D Printers: A radical change to the experimental section of a paper! 38
    39. 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 16/05/2014 The future of laboratory data 39
    40. 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. 16/05/2014 The future of laboratory data 40
    41. 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 16/05/2014 The future of laboratory data 41 ITaaU Network meeting 19 & 20th June Southampton Hilton
    42. 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 The future of laboratory data16/05/2014 42

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