1. Mining Bioscience Literature
Peter Murray-Rust,
University of Cambridge and TheContentMine
SynBio, Cambridge UK, 2015-05-18
Much Scientific Data lies hidden in text and images, in articles, theses,
reports, patents, lab-books…
The ContentMine has Open collaborative tools that anyone can use to
find facts and re-use for their own research

2. 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

3. Scientific and Medical publication (STM)[+]
• World Citizens pay $400,000,000,000…
• … for research in 1,500,000 articles …
• … cost $300,000 each to create …
• … $7000 each to “publish” [*]…
• … $10,000,000,000 from academic libraries …
• … to “publishers” who forbid access to 99.9% of citizens of
the world …
• 85% of medical research is wasted (not published, badly
conceived, duplicated, …)
[+] Figures probably +- 50 %
[*] arXiV preprint server costs $7 USD per paper

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

5. Facts Marked by “non-scientists” in ContentMine workshops
With Wikipedia everyone can be a scientist

6. ContentMine Workshops and
Hackdays
Open Science Brazil, 2014-08
Easily distributed software
Get started in 30 mins
Build application
in a morning
Start simple: bagOfWords, Stemming, Regex, templates

7. Oxford 2013
Berlin 2014
Delhi 2014
Jenny Molloy with mascot AMI

8. 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

9. Workshops
(1-hour -> full day or more)
2014-May->Nov
• Budapest/Shuttleworth
• Leicester Univ
• Electronic Theses and Dissertations
• Austrian Science Fund AT
• OKFest DE
• Eur. Bioinformatics Institute
• Open Science Rio de Janeiro BR
• Sci DataCon , Delhi IN
• Univ of Chicago US
• OpenCon 2014, Wash DC. US
• JISC , London
2015
• LIBER
• Cochrane
• BL
• Wellcome Trust (April)
• WHO
Collaborators
• Wikimedia/Wikidata
• Mozilla
• Open Knowledge
• LIBER (European Research Libraries)
• British Library
• Wellcome Trust
• EBI (Eur. Bioinf. Inst.)
• JISC
• Open Access Button
• SPARC
• Creative Commons
• CORE
• EuropePubmedCentral

10. 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

11. 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

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

13. 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

14. • 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

15. 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

16. 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

17. PLoSONE BMC
1
BMC
2
Closed1 Closed2Hybrid
CATalog
Enhanced annotated
articles
FACTSFACTS
Daily Crawl
Crawl … Scrape … Normalize … Mine
Linked OpenData
Semantic
Scientific Objects
2000-5000
Articles

18. CORE Repository UK

19. PLoSONE BMC
1
BMC
2
Closed1 Closed2Hybrid
CATalog
FACTS
Daily Crawl
Crawl … Scrape … Normalize … Mine
Open3 Closed3
Selected
Retrospective
REPO
Articles
Theses
Reports
Patents
FACTS

20. Peter
Murray-Rust
BMC publisher
Blue Obelisk paper (20
co-authors)
Sub-network
From CATalog

21. Phytochemistry extraction
O. dayi
“volatile composition of “
A.sibeiri
A. judaica
Displayed by CAT (CottageLabs)

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

28. Parsing chemical sentences
This could be extended to much other scientific language

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

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

31. 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.

32. Ln Bacterial load per fly
11.5
11.0
10.5
10.0
9.5
9.0
6.5
6.0
Days post—infection
0 1 2 3 4 5
Bitmap Image and Tesseract OCR

33. UNITS
TICKS
QUANTITY
SCALE
TITLES
DATA!!
2000+ points

34. Dumb PDF
CSV
Semantic
Spectrum
2nd Derivative
Smoothing
Gaussian Filter
Automatic
extraction

35. 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

36. 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

37. 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

38. POSSIBLE USES
• Indexing/searching the literature; G***** for science
• Current awareness; alerts and practices
• Extraction and re-use of facts; re-computation
• Multidisciplinary integration; co-occurrence
• Compliance with funder/institution policies
• Managing your Research Data!
• Finding similar and complementary colleagues
• Reproducibility, checking data and avoiding fraud

39. ContentMine Workshops and
Hackdays
Open Science Brazil, 2014-08
Easily distributed software
Get started in 30 mins
Build application
in a morning
Start simple: bagOfWords, Stemming, Regex, templates

40. Join our Open-Source community at
http://www.contentmine.org