Many scientists have to extract many facts out the scholarly literature - to evaluate other work or to extract useful collections of facts. This shows the approach, especially for systematic reviews of animal or clinical trials
Automatic Extraction of Science and Medicine from the scholarly literature
1. Automatic Extraction of Science and
Medicine from the scholarly literature
Peter Murray-Rust
contentmine.org
CAMARADES group UK, Edinburgh, 2015-05-27
• OPEN Platform for Machines+humans to
automatically “read” the STM literature and
extract facts
• Grow communities and give everyone the tools
and know-how to mine
2. Background
• Contentmine aims to make large areas of scientific fact
OPEN (100 million facts/year)
• We’re working with WellcomeTrust, Europe
PubMedCentral, etc.
• A politically “hot” area (Hargreaves legislation, EU activity)
• 2015 WellcomeTrust workshop on TDM and Neuroscience;
“rough consensus” on what was needed.
• Day workshop at Cochrane, UK (Amy Price, Anna Noel Storr,
Ben Goldacre)
• In the last few months we’ve prototyped a good starting
point… the software is alpha/beta.
3. Regular Expressions for Systematic Reviews of Animal Tests
Preceding Text
Following Text
Extracted term
Today’s Results!! We searched papers for 200 regex-based
Terms and got ca 100 hits per paper
4. Questions we can tackle
• How to we find (mentions of) clinical/animal trials?
• Is a document a trial?
• What is the subject of the trial?
• What is the methodology used?
• Does the design and practice conform to
CONSORT/ARRIVE?
• 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?
5. 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
7. 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
8. “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”
9. 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)
10. 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
11. • “creative use of these large data sets in the US health care sector
could generate more than $300bn in value per annum” [MGI,
McKinsey]
• Gartner Inc. has identified 'Big Data' and 'Next-Generation
Analytics' as two of the 'Top 10 Strategic Technologies' for 2012.
• Given the volume of text generated by business, academic and
social activities – in for example competitor reports, research
publications or customer opinions on social networking sites – text
mining is, however, highly important. [JISC]
• there are some tasks that simply could not be achieved without
using text mining. For example, a major pharmaceutical company
used text mining tools to evaluate 50,000 patents in 18 months.
This would have taken 50 person years to achieve manually,
meaning that it would not even have been contemplated. [JISC]
“Big Data – and Analytics (ContentMining)
12. Prof. Ian Hargreaves (2011): "David Cameron's
exam question”: "Could it be true that laws
designed more than three centuries ago with the
express purpose of creating economic incentives
for innovation by protecting creators' rights are
today obstructing innovation and economic
growth?”
“yes. We have found that the UK's intellectual
property framework, especially with regard to
copyright, is falling behind what is needed.” "Digital
Opportunity" by Prof Ian Hargreaves - http://www.ipo.gov.uk/ipreview.htm. Licensed under CC BY 3.0 via Wikipedia -
https://en.wikipedia.org/wiki/File:Digital_Opportunity.jpg#/media/File:Digital_Opportunity.jpg
13. PUBLISHER TDM LICENCE INITIATIVES
GENERALLY DO NOT HELP
• Publishers have started offering their own TDM licences and policies
• Their licences often impose unfair (and in the case of the UK, unenforceable)
constraints on researchers’ freedom to exploit TDM, e.g., requiring users to
employ publisher’s API, putting unnecessary restrictions on how much can be
copied, or how fast it can be copied.
• Why “unenforceable”? Because, as noted earlier, UK law specifically states
that any contract or licence term that prevents anyone from doing TDM in the
manner prescribed in the new exception shall be deemed null and void.
• Really need a test case on these attempted restrictions.
• Springer and Royal Society offer generous TDM provisions.
• So why are so many publishers offering restrictive licences in the UK? Maybe
they hope licensees are ignorant of the strength of the new law, or the
publishers in fact don’t know about it. So they are either deliberately
misleading, or ignorant
Prof Charles Oppenheim and contentmine.org
21. Machine-Human symbioses
• Wikipedia
• Open StreetMap
• Google
We aim to make it trivial for a human+machine
to mine the scientific literature.
By building Communities
22. 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
23. Facts Marked by “non-scientists” in ContentMine workshops
With Wikipedia everyone can be a scientist
25. 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
Upcoming
• 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
26. • 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
38. 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.
39.
40. 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
44. 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)
48. 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
49. contentmine.org proposed Services
• Workshops
• Repository indexing
• Funder Compliance
• Publication enhancement
• Extraction of scientific data
• Creation of community-led groups