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
Scholarly infrastructure becomes closed
No accountability for monitoring and control
The Digital Enlightenment: some of my icons
Diderot, Paris, 1751
Berkeley, US, 1966 Paris, 1968
UK, 1969-73
["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
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
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
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.
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
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,ArtLiterature
Social
Knowledgebases
RDF triples
Liberation Software
Steve Coast developed OpenStreetMapto challenge the monopoly of the UK Ordnance Survey
The Right to Read is the Right to Mine
http://contentmine.org
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
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
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
What is “Content”?
http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0111303&representation=PDF CC-BY
SECTIONS
MAPS
TABLES
CHEMISTRYTEXT
MATH
contentmine.org tackles these
“nuggets” in a scientific paper
quantity
units
Value ranges
Humans aren’t designed to mine this … chemical
project places
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
• 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
quickscrapeCrawlFeed
Norma Index &Transform
XML
URL
DOI
Scientificliterature
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
CORE Repository UK
HAL repository FR
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)
Bag of Words
Theses from HAL repository
Species
Regex for Clinical Trials
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?
How a machine reads a chemical thesis
nodes are compounds; arrows are reactions
Natural Language Processing
Part of speech tagging (Wordnet, Brown Corpus, etc.)
Parsing chemical sentences
http://chemicaltagger.ch.cam.ac.uk/
• Typical
Typical chemical synthesis
Automatic semantic markup of chemistry
Could be used for analytical, crystallization, etc.
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.
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)
Evolution of ultraviolet vision in the largest avian radiation - the passerines Anders Ödeen 1* , OlleHåstad 2,3 and Per Alström 4
HTML
Styles , superscripts
And diåcriticspreserved!
AMI
Turdus iliacusTaeniopygia guttataSerinus canariaLanius excubitorMelopsittacus undulatusPavo cristatusSturnus vulgarisDolichonyx oryzivorusFicedula hypoleucaVaccinium myrtillusFalco tinnunculus
TurdusPomatostomusLeothrixAmytornisAcanthisittaOrthonyx x 2MalurusCnemophilus x 4Philesturnus x 2Motacilla x 2Toxorhampus x 2
Typical phylo tree: 60 nodes, complex and miniscule annotation, vertical text, hyphenation and valuable branch lengths. AMI extracts ALL
AcanthisittidaeAcanthizidaeAcrocephalidaeCallaeidaeCampephagidaeCnemophilidaeCorvidae
0.840.910.930.95
AcanthisittaAcrocephalusAiluroedusAiluroedusAmytornisCamptostoma
AMI
23.1234.5437.2138.55
Posteriorprobability
AMI can MEASUREBranch lengths!
NexML
Genus Family
HTML
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
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
Additional material on Open Notebook Science (not presented)
Free/Open Software DevelopmentEngineered repository
Worldcommunity
CODErewrite
validate
CODEfork
CODE
Re-use
CODERe-use
Github, BitBucketStackOverflow,Apache
inspires
OSI
Example: ContentMine athttp://github.com/ContentMine/quickscrape
Sophie Kershaw, Panton Fellow, Training PhD Students
“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
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
http://michaelnielsen.org/blog/reinventing-discovery/
http://en.wikipedia.org/wiki/Reinventing_Discovery
TOOLS
Open Notebook Science
Open engineeredrepository
Worldcommunity
INSTRUMENT
validate
merge
MODELCODE
DATA
DATAknowledge
calibrate
Problems are solved communally; Nothing is needlessly duplicated; “publication“ is continuous
Machines and humansWorking together
CC-BY
“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”
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)
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)
Panton Authors and Fellows