Published on Apr 21, 2015 by PMR Theses represent a huge amount of untapped value. We show how contentmine.org technology can be used to mine them and extract knowledge

1. Scholarly Infrastructure: Open or Closed?
Peter Murray-Rust*,
University of Cambridge and OpenKnowledge
DRTD-SHS, Lille, FR 2015-04-21
We can build an Open discovery and re-use system.
Theses represent huge untapped communal knowledge.
Bliss was it in that dawn to be alive,
But to be young was very heaven!
Wordsworth on the French Revolution

2. Scholarly infrastructure becomes closed
No accountability for monitoring and control

3. The Digital Enlightenment: some of my icons
Diderot, Paris, 1751
Berkeley, US, 1966 Paris, 1968
UK, 1969-73

4. ["How We Stopped SOPA”:
This bill ... shut down whole websites. Essentially, it stopped Americans from
communicating entirely with certain groups....
I called all my friends, and we stayed up all night setting up a website for this new group,
Demand Progress, with an online petition opposing this noxious bill.... We [got] ... 300,000
signers.... We met with the staff of members of Congress and pleaded with them.... And then
it passed unanimously....
And then, suddenly, the process stopped. Senator Ron Wyden ... put a hold on the
bill.[48][49]
He added, "We won this fight because everyone made themselves the hero of their own
story. Everyone took it as their job to save this crucial freedom.”
Robert Swartz: "Aaron was killed by the government, and MIT betrayed all of its basic
principles."[116]
Aaron Swartz

5. Some Children
of the Digital Enlightenment
• David Carroll & Joe McArthur: OAButton
• Rayna Stamboliyska & Pierre-Carl Langlais
• Jon Tennant
• Ross Mounce
• Jenny Molloy
• Erin McKiernan
• Jack Andraka
• Michelle Brook
• Heather Piwowar
• TheContentMine Team
• Rufus Pollock
• Jonathan Gray
• Sophie Kay
Jean-Claude Bradley [1] a chemist
developed Open notebook science;
making the entire primary record of a
research project publicly available
online as it is recorded. (WP)
J-C promoted these ideas with
UNDERGRADUATE scientists.
[1] Unfortunately J-C died in 2014;
we held a memorial meeting in
Cambridge
Sophie
Kay

6. http://www.nytimes.com/2015/04/08/opinion/yes-we-were-warned-about-
ebola.html
We were stunned recently when we stumbled across an article by European
researchers in Annals of Virology [1982]: “The results seem to indicate that
Liberia has to be included in the Ebola virus endemic zone.” In the future,
the authors asserted, “medical personnel in Liberian health centers should be
aware of the possibility that they may come across active cases and thus be
prepared to avoid nosocomial epidemics,” referring to hospital-acquired
infection.
Adage in public health: “The road to inaction is paved with research
papers.”
Bernice Dahn (chief medical officer of Liberia’s Ministry of Health)
Vera Mussah (director of county health services)
Cameron Nutt (Ebola response adviser to Partners in Health)
A System Failure of Scholarly Publishing

7. Open Scholarship must build its own
discovery system before it is too late
Communities of Practice + software:
• Wikip(m)edia
• Open Street Map
• Open Corporates
Theses are under OUR control and hugely valuable.

8. eTheses
• Citizens pay $20,000,000,000*…
• … for research in 200,000 science theses*…
• … cost $100,000 each to create* …
• … re-use ??? (near zero)
• … Value???
• *Please challenge these numbers…
• NOTE: we pay publishers $15,000,000,000 for
journals and APCs

9. Linked Open Data – the world’s knowledge
very little physical science and THESES?? 
http://upload.wikimedia.org/wikipedia/commons/3/34/LOD_Cloud_Diagram_as_of_September_2011.png
DBPedia
BIO
Comp
Lib
PDB
Ontologies
GOV
GOV.uk
Music,
Art
Literature
Social
Knowledge
bases
RDF
triples

10. Liberation Software
Steve Coast developed OpenStreetMap
to challenge the monopoly of the UK Ordnance Survey

11. The Right to Read is the Right to Mine
http://contentmine.org

12. OUR TEAM
@jenny_molloy
Ross Mounce
@rmounce
Richard Smith-
Unna
@blahah404
Stephanie Smith-
Unna
@treblesteph
Jenny Molloy
Mark
MacGillivray
@cottagelabs
Peter Murray-
Rust
@petermurrayrust
Charles Oppenheim
@CharlesOppenh
Graham
Steel
@McDawg

13. https://en.wikipedia.org/wiki/Irrigation#mediaviewer/File:Pump-
enabled_Riverside_Irrigation_in_Comilla,_Bangladesh,_25_April_2014.jpg CC BY-SA 3.0
Daily Stream of 100,000 Open Facts
Twitter?Indexed by CAT
http://catalogue.cottagelabs.com/browsehttp://catalogue.cottagelabs.com/graph

14. Content-Mining (TDM*)
• Now COMPLETELY LEGAL IN UK since 2014-06-01
(“Hargreaves”)…
• … Whatever the publishers tell you. Do NOT sign
their APIs
• UK can legally IGNORE contractual restrictions
• Movement to extend this to Europe (Julia Reda,
MEP proposal)
• And STM publishers are spending millions to stop
us
*Text and Data Mining

15. What is “Content”?
http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.01113
03&representation=PDF CC-BY
SECTIONS
MAPS
TABLES
CHEMISTRY
TEXT
MATH
contentmine.org tackles these

16. “nuggets” in a scientific paper
quantity
units
Value ranges
Humans aren’t designed to mine this … 
chemical
project places

17. What is “Content”?
Emily Sena (neuroscience.ed.ac.uk) spends
half a day digitising a diagram like this
ContentMine will soon be able to do it in 1 second

18. • CRAWL the web for scientific documents
(articles, grey literature, repositories)
• quickSCRAPE pages (text, graphics, images, data)
• NORMA-lize page to semantic form
…Open semantic science …
• MINE pages with your methods and tools (AMI)
• CAT-alogue results in searchable index
• Automate daily process (CANARY)
contentmine.org Infrastructure

19. quickscrape
Crawl
Feed
Norma Index &
Transform
PDF
XML
URL
DOI
Scientific
literature
Repositories DOC
CSV
sHTML
Plugins
Regex
SequencesSpecies
Bespoke
Scrapers
XPathPer-Journal
Taggers
Per- Journal
MetadataChemistry
Phylogenetics Farming
AMI
BadHTML
OCR
Diagrams
Open NORMA-lized Scientific
Literature + Facts
CANARY pipeline
CAT-alogue index

20. CORE Repository UK

21. HAL repository FR

22. Retrieval/Extraction Technologies
• Bag Of Words https://en.wikipedia.org/wiki/Bag-of-words_model)
• Term-Frequency Inverse-Document-Frequency
https://en.wikipedia.org/wiki/Tf%E2%80%93idf
• Regular Expressions
• Templates (Information Extraction)
• Natural Language Processing (NLP)
• Image processing and mining
• Lookup (Wikidata, Bioscience databases)

23. Bag of Words
Theses from HAL repository

24. Species

25. Regex for Clinical Trials

26. CLINICAL TRIALS
How to we find (mentions of) clinical trials?
Is a document a (clinical) trial?
What is the subject of the trial?
What is the methodology used? How many/long?
Does the design and practice conform to CONSORT?
What are the outcomes?
Can we extract specific re-usable information?
Who are involved? (researchers, sponsors, patients?)
Has a proposed trial been completed and reported?

27. How a machine reads a chemical thesis
nodes are compounds; arrows are reactions

28. Natural Language Processing
Part of speech tagging (Wordnet, Brown Corpus, etc.)

29. Parsing chemical sentences

30. http://chemicaltagger.ch.cam.ac.uk/
• Typical
Typical chemical synthesis

31. Automatic semantic markup of chemistry
Could be used for analytical, crystallization, etc.

32. Open Content Mining of FACTs
Machines can interpret chemical reactions
We have done 500,000 patents. There are >
3,000,000 reactions/year. Added value > 1B Eur.

33. AMI https://bitbucket.org/petermr/xhtml2stm/wiki/Home
Example reaction scheme, taken from MDPI Metabolites 2012, 2, 100-133; page 8, CC-BY:
AMI reads the complete diagram,
recognizes the paths and
generates the molecules. Then
she creates a stop-fram animation
showing how the 12 reactions
lead into each other
CLICK HERE FOR ANIMATION
(may be browser dependent)

34. Evolution of ultraviolet
vision in the largest avian
radiation - the passerines
Anders Ödeen 1* , Olle
Håstad 2,3 and Per Alström 4
PDF 
HTML 
Styles , superscripts
And diåcritics
preserved!
AMI

35. PDF 
Turdus iliacus
Taeniopygia guttata
Serinus canaria
Lanius excubitor
Melopsittacus undulatus
Pavo cristatus
Sturnus vulgaris
Dolichonyx oryzivorus
Ficedula hypoleuca
Vaccinium myrtillus
Falco tinnunculus
Turdus
Pomatostomus
Leothrix
Amytornis
Acanthisitta
Orthonyx x 2
Malurus
Cnemophilus x 4
Philesturnus x 2
Motacilla x 2
Toxorhampus x 2

36. Typical phylo tree: 60 nodes, complex and miniscule annotation,
vertical text, hyphenation and valuable branch lengths. AMI extracts ALL

37. Acanthisittidae
Acanthizidae
Acrocephalidae
Callaeidae
Campephagidae
Cnemophilidae
Corvidae
0.84
0.91
0.93
0.95
Acanthisitta
Acrocephalus
Ailuroedus
Ailuroedus
Amytornis
Camptostoma
AMI
23.12
34.54
37.21
38.55
Posterior
probability
AMI can MEASURE
Branch lengths!
NexML
Genus Family
HTML

38. https://blogs.ch.cam.ac.uk/pmr/2014/06/25/content-mining-we-can-now-
mine-images-of-phylogenetic-trees-and-more/ for story of extraction
Thinning Topology
Serialization
Newick

39. Problems
• Cannot do handwriting
• Scanned documents give poorer results
• The older the document the poorer the result
• Tables are a major problem
• Always try to get the original document
• XML better than > Word better than > PDF
• Vector images >> PNG > JPEG
• Maths, chemistry are specialist

40. Additional material on Open Notebook
Science (not presented)

41. 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

42. Sophie Kershaw, Panton Fellow, Training PhD Students

43. “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

44. 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

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

46. 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

47. “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”

48. 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 Swartz (1986-2013)

49. 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)

50. Panton Authors and Fellows