Open Notebook Science

Open Notebook Science
Peter Murray-Rust* and Michelle Brook,
Open Knowledge and University of Cambridge
FWF, Vienna, AT, 2014-06-03
*Shuttleworth Fellow 2014-5

Overview
• Most scientific data is lost; costs many billions…
• … AND LIVES. Closed Data Means People Die
• Human problem; lack of vision + active opposition.
• Fully open data can change this
• Appreciation of Jean-Claude Bradley’s work
• Panton Fellows (Ross Mounce, Sophie Kershaw)
• Content Mining - interim solution (Hargreaves UK)
• Digital Enlightenment or Digital Darkness?
• WHAT CITIZENS CAN and MUST DO

[at Research Data Alliance, we are entering a new “era of open science”, which will be “good
for citizens, good for scientists and good for society”.
She explicitly highlighted the transformative potential of open access, open data, open
software and open educational resources – mentioning the EU’s policy requiring open access
to all publications and data resulting from EU funded research.
http://blog.okfn.org/2013/03/21/we-are-entering-an-era-of-open-science-says-eu-vp-neelie-
kroes/#sthash.3SWDXDE6.dpuf
RCUK
Wellcome
ERC
NSF
FWF…
require
fully OPEN

PMR’s Tribute
Planned Memorial Meeting
July 14th 2014 Cambridge
OPEN NOTEBOOK SCIENCE

Award of Blue Obelisk
Jean-Claude Bradley Egon Willighagen

Traditional Research and Publication
“Lab” work paper/th
esis
Write
rewrite
Re-experiment
publish
???
Validation??
DATA
output “belongs”
to publisher

Elsevier wants to control Open Data
[asked by Michelle Brook]

Free/Open Software Development
Engineered
repository
World
community
CODE
rewrite
validate
CODE
fork
CODE
Re-use
CODE
Re-use
Github, BitBucket
StackOverflow,
Apache
inspires
OSI
Example: ContentMine at
http://github.com/ContentMine/quickscrape

Open Source software inspires Open Science
Jean-Claude Bradley 2006

Open Notebook Science, ONS

And spectra were included as well

TOOLS
Open
engineered
repository
World
community
INSTRUMENT
validate
merge
MODEL
CODE
DATA
DATA
knowledge
calibrate
Problems are solved communally;
Nothing is needlessly duplicated; “publication“ is
continuous ; data are SEMANTIC
Machines
and humans
Working
together

Mat Todd, University of Sydney: Antimalarial

Medicinal Chemistry:
Make thousands of
similar compounds
till you get one
suitable;
O Instead of N
is 300 times better

The economic value of data
• I believe that we spend globally ca 400 billion
USD / yr on public research.
• The outputs include:
– Knowledge / papers / patents
– Organizations
– People
– Materials
– Data – many billions/year and much is lost

US Taxpayers spend 139 Billion USD / yr
on Scientific Research
4 Billion USD on human genome
yielded 800 Billion USD and 4 M job-years

…three problems—flawed design, non-
publication, and poor reporting—together
meant >85% of research funds were wasted, a
global total loss >100 billion USD per year.
[Lancet 2009]
[Even more] waste clearly occurs after
publication: from poor access, poor
dissemination, and poor uptake of the findings
of research. [PLOS Medicine 2014-05-27]
Bad publication wastes science

Citizens pay $400,000,000,000
Value : ???
… cost $300,000 each to create
… for research in 1,500,000 articles
$7000 each to “publish” costs
$10,000,000,000
“publishers” forbid access to 99.9% of
citizens of the world

Where is the Digital Enlightenment?
• Science is done in C20th ways …
• …communicated in C19th ways …
• … losing the power of C21st

http://michaelnielsen.org/blog/reinventing-
discovery/
http://en.wikipedia.org/wiki/Reinventing_Discovery

http://gowers.wordpress.com/2013/11/03/dbd1-initial-post/
http://polymathprojects.org/2013/11/04/polymath9-pnp/#comments
The Polymath project
Tim Gowers and the world

“Free” and “Open”
• "Free software is a matter of liberty, not price.
’free speech', not 'free beer'”. (R M Stallman)
• “A piece of data or content is open if anyone is
free to use, reuse, and redistribute it”
(OKFN)http://opendefinition.org/
• “open” (access) has multiple incompatible “definitions”. Major split
is “human eyeballs” vs copying and machine “reusability”
• “Open” is a marketing term for publishers, who frequently (often
deliberately) do not grant full Openness.
“Gratis” vs “Libre”

4 Freedoms (Richard Stallman)
• Freedom 0: The freedom to run the program for any purpose.
• Freedom 1: The freedom to study how the program works, and
change it to make it do what you wish.
• Freedom 2: The freedom to redistribute copies so you can help
your neighbor.
• Freedom 3: The freedom to improve the program, and release
your improvements (and modified versions in general) to the
public, so that the whole community benefits.
"I’ve spent a third of my life building software based on Stallman’sfour freedoms, and
I’ve been astonished by the results. WordPress wouldn’t be here if it weren’t for those
freedoms, and it couldn’t have evolved the way it has.”
- Matt Mullenweg, co-creator of WordPress

Critical Historical Open Events
• Free Software Foundation (RMS,
1985) and Linux (Torvalds, 1991)
• The World Wide Web (TBL, 1991)
• The human genome (1990-2001)
The life of Aaron Swarz (1986-2013)

https://en.wikipedia.org/wiki/Bermuda_Principles
• Automatic release of sequence assemblies larger than 1
kb (preferably within 24 hours).
• Immediate publication of finished annotated
sequences.
• Aim to make the entire sequence freely available in the
public domain for both research and development in
order to maximise benefits to society.

http://www.budapestopenaccessinitiative.org/read
… an unprecedented public good. …
… completely free and unrestricted access to [peer-
reviewed literature] by all scientists, scholars, teachers,
students, and other curious minds. …
…Removing access barriers to this literature will
accelerate research, enrich education, share the
learning of the rich with the poor and the poor with
the rich, make this literature as useful as it can be, and
lay the foundation for uniting humanity in a common
intellectual conversation and quest for knowledge.
(Budapest Open Access Initiative, 2003)

Authors don’t deposit data (Ross Mounce)

Restrictions on Re-use of Crystallographic data
NOTE: The CCDC is based on data contributed by
scientists as part of publication and validation

Mendeley
From Wikipedia, the free encyclopedia
• … a social media site used by many scientists
to store metadata …
• … purchased by Elsevier in 2013
• David Dobbs, in The New Yorker, described
motive as:
– to acquire its user data,
– to destroy or coöpt an open-science icon that
threatens its business model.
• PM-R: Mendeley can also Snoop and Control

Panton Principles for Open Data in
science(2010)
• PUBLISH YOUR DATA OPENLY
• …make an explicit and robust statement of your wishes.
• Use a recognized waiver or license that is appropriate for
data.
• open as defined by the Open Knowledge/Data Definition
(… NOT non-commercial)
• Explicit dedication of data … into the public domain via
PDDL or CCZero
Peter Murray-Rust, Cameron Neylon, Rufus Pollock, John
Wilbanks

Sophie Kershaw, Panton Fellow :
Doctoral Training in Oxford

“Train a new generation of data scientists
and broaden public understanding”
“Riding The Wave”
European Commission
October 2010

Rotation-Based Learning (RBL)
Phase 1: Initiator
• No communication
permitted between groups
• Attempt to reproduce
existing literature
• Deliver a coherent research
story by the end of Phase 1
Phase 2: Successor
• Communication between
groups still prohibited
• Validate and develop the
inherited research story
• Critique your predecessors
• Role of research producer vs. research user
• Can this approach help to foster awareness of reproducibility issues?
Throughout Phases 1 & 2:
• Daily lectures on open
science culture & techniques
• First-hand application to own
research work
• Version control using GitHub
• Daily group supervision

“Do you think you would be
more confident in the future
about trying to apply Open
techniques to your work..?”
• 50% Yes, by myself
• 41% Yes, with help/guidance
• 9% No opinion/neutral
• 0% No

Ross Mounce (Bath), Panton Fellow
• Sharing research data:
http://www.slideshare.net/rossmounce
• How-to figures from PLOS/One [link]:
Ross shows how to bring figures to life:
• PLOSOne at http://bit.ly/PLOStrees
• PLOS at http://bit.ly/phylofigs (demo)

TOOLS
Open
engineered
repository
World
community
INSTRUMENT
validate
merge
MODEL
CODE
DATA
DATA
knowledge
calibrate
Problems are solved communally;
Nothing is needlessly duplicated; “publication“ is
continuous
Machines
and humans
Working
together
CC-BY

Traditional Research and Publication
esis
Write
rewrite
Re-experiment
publish
???
Validation??
DATA
output “belongs”
to publisher
Is there anything we can do with this?

Content Mining (TDM)
esis
Write
publish
???
DATA
Intelligent software
to read scientific papers
DATA
Publishers have tried to stop us mining it.
On 2014-06-01 IT BECAME LEGAL IN UK!
The Right To Read Is The Right To Mine

Content Mining
• 1,000,000 papers/year => 3,000 / day => 2 /min
• 10,000+ phylogenetic trees (Ross Mounce, BBSRC)
• 20,000 chemical reactions / day
• >> 1 million graphs, plots, bar charts, statistics
• Possible on a laptop
• http://contentmine.org

AMI2: High-throughput extraction of
semantic chemistry from the scientific
literature
Andy Howlett, Mark Williamson, Peter Murray-Rust,
Unilever Centre, Cambridge

AMI2 is a framework that can extract
semantic data from the scientific
literature.

Visitor Design Pattern/Example
Visitor= something that extracts a specific type of data
SpeciesVisitor, ChemVisitor, PhylogeneticTreeVisitor,
GeoLocationVisitor, ClinicalTrialVisitor …
Visitable= something that can have specific data extracted
PDF, SVG, Table

ChemistryVisitor
Can interpret diagram or look up chemistry in PubChem or ChEBI

C) What’s the problem with this spectrum?
Org. Lett., 2011, 13 (15), pp 4084–4087
Original thanks to ChemBark

After AMI2 processing…..
… AMI2 has detected a square

Thanks
• BBSRC for PLUTo project (Bath)
• Unilever Research for PhD (Andy Howlett)
• TechnologyStrategyBoard / CambridgeIP (PDRA Mark Williamson)
• Shuttleworth Foundation (Fellowship PM-R)
• Julian Huppert MP and David Willetts (support for Hargreaves
copyright reform)
• Christoph Steinbeck (EBI) Metabolights
• The ContentMine team (Michelle Brook, Ross Mounce, Jenny
Molloy, Richard Smith-Unna, CottageLabs)
• The Blue Obelisk
• Open Knowledge
• Apache PDFBox and all F/LOSS software authors
• Unilever Centre and University of Cambridge

CLOSED ACCESS MEANS PEOPLE DIE
• Create Open Notebook Science in your discipline
• Actively release data into Public Domain.
• Actively campaign against any re-use restrictions
(including CC-BY-NC)
• Refuse to work with closed organizations
• Convince Academia to Open its doors
CLOSED DATA MEANS PEOPLE DIE

http://usefulchem.blogspot.co.uk/2011/06/quest-to-determine-melting-point-of-4.html
http://www.slideshare.net/jcbradley/minisymp2011-bradley
https://impactstory.org/BlueObelisk
http://www.slideshare.net/rossmounce/sharing-reusable-phylogenetic-data-were-not-
there-yet
http://footnote1.com/the-exploitative-
economics-of-academic-publishing/
http://web.ornl.gov/sci/techresources/Human
_Genome/publicat/BattelleReport2011.pdf
https://www.youtube.com/watch?v=BN8UjUL
NG9A&feature=youtube_gdata mins 5-9
Some references

Open Notebook Science

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