Open Knowledge and University of Cambridge European Bioinformatics Institute

Open Data
Peter Murray-Rust*,
Open Knowledge and University of Cambridge
European Bioinformatics Institute, UK, 2014-05-15
*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 as partial solution (Hargreaves UK)
• WHAT YOU MUST DO

Elsevier wants to control Open Data

Award of Blue Obelisk
Jean-Claude Bradley Egon Willighagen

Conventional Research
“Lab” work paper/th
esis
Write
rewrite
Re-experiment
publish
???
Validation??
DATA
All your data are
belong to publisher

Free/Open Software Development
Engineered
repository
World
community
CODE
rewrite
validate
CODE
fork
CODE
Re-use
CODE
Re-use
Github, BitBucket
Stackoverflow,
Apache
e.g. Chem4Word (M-R group)
Outercurve repository,
Now developed by ex-pharma s/w
And interfaced to ChemDoodle
inspires
OSI

Open Source software inspires Open Science
Jean-Claude Bradley 2006

Open Notebook Science, ONS

And spectra were included as well

https://www.youtube.com/watch?v=BN8UjUL
NG9A&feature=youtube_gdata
Jean-Claude Bradley talking in 2013

TOOLS
Open Science
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
• JC was a pioneer in open science, and uncompromising
about its importance. We had so many productive
interactions over the years, starting from the end of
January 2006, when we started our open chemistry project
on The Synaptic Leap (JC was the first to comment!) and JC
posted his very first experiment online at Usefulchem. I
remember starting to think about how to do completely
open projects, looking around the web in 2005 to see if
anything open was going on in chemistry, and coming
across JC's lone voice, and I thought "Wow, who is this
guy?" He had dedication and integrity - we'll all miss him.
2014-05-15 (Mail to PM-R)

Mat Todd, University of Sydney: Antimalarial

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

http://michaelnielsen.org/blog/reinventing-
discovery/

https://en.wikipedia.org/wiki/Reinventing_Discovery
Michael Neilsen
Kasparov versus the World, The Wisdom of Crowds, various online collaborative projects
InnoCentive, collective intelligence, Paul Seabright's economic theory, online chat
History of Linux, Open Architecture Network, Wikipedia, MathWorks' computer programming
contest
communication in small groups, particularly as studied by Stasser and Titus; praxis of science; a
discussion of communication among scientists
Don R. Swanson and Literature-based discovery, predicting influenza with Google searches,
Sloan Digital Sky Survey, Allen Institute for Brain Science, Ocean Observatories Initiative, Human
Genome Project, Google Translate
Democratizing Science Galaxy Zoo, Foldit, citizen science, eBird, open access, arXiv, PLoS
The Challenge of Doing Science in the Open Complexity Zoo, academic publishing
The Open Science Imperative Open science, academic journal publishing reform, SPIRES
appendix - The problem solved by the Polymath Project

“Free” and “Open”
• "Free software is a matter of liberty, not price. ’free
speech', not 'free beer'”. (RMS)
• “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.

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.
(BOAI, 2003)

Mendeley
From Wikipedia, the free encyclopedia
• Mendeley – 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

Authors don’t deposit data (Ross Mounce)

NOTE: RSC have always published raw crystal data as
“CC0” and the enhanced data is openly
available

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

(auth: Mark Hahnel in response to our debates)

Panton Principles for Open Data in
science(2010)
• …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

Sophie Kershaw, Panton Fellow :
Doctoral Training in Oxford

Reproducibility?
Begley & Ellis (2012)
Nature 483, 531-533
Image shown is from front page of Begley & Ellis
(2012), produced by the Nature Publishing Group

“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 Notebook Science
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

Content Mining
“Lab” work paper/th
esis
Write
publish
???
DATA
Intelligent software
To read scientific papers
DATA
Despite the inefficiency and loss much unused data remains
In published articles. Publishers have tried to stop us mining it.
On 2014-06-01 IT WILL BE LEGAL IN UK!

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
Anyone interested in data from clinical trials papers?

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)
• TSB / Cambridge IP (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
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

TOOLS
Open Science
Open
engineered
repository
World
community
INSTRUMENT
validate
merge
MODEL
CODE
DATA
DATA
knowledge
calibrate
“Publication” is continuous and all “curious minds”
can be involved.

Open Knowledge and University of Cambridge European Bioinformatics Institute

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