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


University of Southampton Library Resources


Open Data


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


Data Curation in the Chemical Sciences


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

Intelligent Open Access to Data The future of laboratory data16/05/2014

10

StructureGate


THE NARRATIVE

What is the story? What is the why?


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’


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

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



The Trove Software

17

BlogMyData Project - Godiva


LabTrove and User defined metadata


A big proportion of our users are not

really adding metadata!

Librarians can help here!


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


http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067460

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


doi: 10.1098/rsta.2005.1630 Phil. Trans.

R. Soc. A 15 August 2005 vol. 363 no.

1833 2075-2095


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


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


Select

entries

(all)

Export as HTML “static”

copy

Zip and send to

repository

LabTrove Notebooks


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!


http://ses.library.usyd.edu.au/handle/2123/10461

Example from Mat Todd

University of Sydney



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”


It is not necessary to change. Survival is not mandatory.

W. Edwards Deming

32


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


eprints.soton.ac.uk

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?



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


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


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.


Join the ITaaU Network+

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• LinkedIn group: IT-as-Utility-Network16/05/2014 The future of laboratory data 41

ITaaU Network meeting 19 & 20th June

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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

ustlg talk: the future of laboratory data: libraries, librarians and digital laboratory notebooks

Science

future of laboratory

future of laboratory

future of experimental

independent laboratory

faradays laboratory

sufficient data

data curation

large amounts of data