Published on Jul 10, 2015 by PMR
Scholarly Publishing wastes huge amounts of valuable science. This presentation to the Public Library of Science suggests how we can work together to put this right
1. The Avoidable Waste of Scholarly Publishing
Peter Murray-Rust*,
ContentMine.org and the University of Cambridge
PLoS, Cambridge, UK 2015-07-09
Scholarly Publishing un/wittingly destroys huge amounts of publicly
funded research.
There are solutions; what is needed is will
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)
• 2-day workshop at Edinburgh on Systematic Reviews of Animal Test
publications
• In the last few months we’ve prototyped a unique Open starting
point, continuously released.
• Can PLoS and ContentMine find constructive ways forward?
3. PM-R’s “first real paper”, doing science by
re-using the results of otherts in a novel way
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. MONROVIA, Liberia — The conventional
wisdom among public health authorities is
that the Ebola virus, which killed at least
10,000 people in Liberia, Sierra Leone and
Guinea, was a new phenomenon, not seen in
West Africa before 2013. (The one exception
was an anomalous case in Ivory Coast in 1994,
when a Swiss primatologist was infected after
performing an autopsy on a chimpanzee.)
The conventional wisdom is wrong. We were
stunned recently when we stumbled across an
article by European researchers in Annals of
Virology: “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.
As members of a team drafting Liberia’s Ebola
recovery plan last month, we systematically
reviewed the literature on Ebola surveillance
since the virus’s discovery in central Africa in
1976. We learned that the virologists who wrote
that report, who were from Germany, had
analyzed frozen blood samples taken in 1978 and
1979 from 433 Liberian citizens. They found that
26 (or 6 percent) had antibodies to the Ebola
virus.
Three other studies published in 1986
documented Ebola antibody prevalence rates of
10.6, 13.4 and 14 percent, respectively, in
northwestern Liberia, not far from its borders
with Sierra Leone and Guinea. These articles,
along with other forgotten reports from the
1980s on antibody prevalence in neighboring
Sierra Leone and Guinea, suggest the possibility
of what some call “sanctuary sites,” or
persistent, if latent, Ebola infection in humans.
Bernice Dahn is the chief medical officer of Liberia’s Ministry of Health, where Vera Mussah
is the director of county health services. Cameron Nutt is the Ebola response adviser to Dr.
Paul Farmer at the nonprofit group Partners in Health.
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
35. catalogue
getpapers
query
Daily
Crawl
EuPMC, arXiv
CORE , HAL,
(UNIV repos)
ToC
services
PDF HTML
DOC ePUB
TeX XML
PNG
EPS CSV
XLSURLs
DOIs
crawl
quickscrape
norma
Normalizer
Structurer
Semantic
Tagger
Text
Data
Figures
ami
UNIV
Repos
search
Lookup
CONTENT
MINING
Chem
Phylo
Trials
Crystal
Plants
COMMUNITY
plugins
Visualization
and Analysis
PloSONE, BMC,
peerJ… Nature, IEEE,
Elsevier…
Publisher Sites
scrapers
queries
taggers
abstract
methods
references
Captioned
Figures
Fig. 1
HTML tables
30, 000 pages/day
Semantic ScholarlyHTML
Facts
36. 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
37. 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?
38. 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
45. catalogue
getpapers
query
Daily
Crawl
EuPMC, arXiv
CORE , HAL,
(UNIV repos)
ToC
services
PDF HTML
DOC ePUB
TeX XML
PNG
EPS CSV
XLSURLs
DOIs
crawl
quickscrape
norma
Normalizer
Structurer
Semantic
Tagger
Text
Data
Figures
ami
UNIV
Repos
search
Lookup
CONTENT
MINING
Chem
Phylo
Trials
Crystal
Plants
COMMUNITY
plugins
Visualization
and Analysis
PloSONE, BMC,
peerJ… Nature, IEEE,
Elsevier…
Publisher Sites
scrapers
queries
taggers
abstract
methods
references
Captioned
Figures
Fig. 1
HTML tables
30, 000 pages/day
Semantic ScholarlyHTML
Facts
46. 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
47. 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
48. Facts Marked by “non-scientists” in ContentMine workshops
With Wikipedia everyone can be a scientist
50. 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
51. • 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
52. catalogue
getpapers
query
Daily
Crawl
EuPMC, arXiv
CORE , HAL,
(UNIV repos)
ToC
services
PDF HTML
DOC ePUB
TeX XML
PNG
EPS CSV
XLSURLs
DOIs
crawl
quickscrape
norma
Normalizer
Structurer
Semantic
Tagger
Text
Data
Figures
ami
UNIV
Repos
search
Lookup
CONTENT
MINING
Chem
Phylo
Trials
Crystal
Plants
COMMUNITY
plugins
Visualization
and Analysis
PloSONE, BMC,
peerJ… Nature, IEEE,
Elsevier…
Publisher Sites
scrapers
queries
taggers
abstract
methods
references
Captioned
Figures
Fig. 1
HTML tables
30, 000 pages/day
Semantic ScholarlyHTML
Facts
64. 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.
65.
66. 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
70. 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)
74. What we can do
• Recognize and promote autonomous sub-
communities
• Engage Early Career Researchers, including
undergraduates and let THEM BUILD the
systems.
• COMMUNALLY build tools for data checking
• Insist on semantic data input, even if it costs
submissions
Hi, I’m here to talk about AMI; a data extraction framework and tool. First, I just want highlight some of key contributors to the projects; Andy for his work on the ChemistryVisitor and Peter for the overall architecture.
In this talk, I’m going to impress the importance of data in a specific format and its utility to automated machine processing. Then I’m going to demonstrate AMI’s architecture and the transformation of data as it flows through the process. I’m going to dwell a little on a core format used, Scalable Vector Graphics (SVG) before introducing the concept of visitors, which are pluggable context specific data extractors. Next, I’m going to introduce Andy’s ChemVisitor, for extracting semantic chemistry data, along with a few other visitors that can process non-chemistry specific data. Finally, I will demonstrate some uses of the ChemVisitor, within the realm of validation and metabolism.