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![["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](https://image.slidesharecdn.com/lille2015-150421041732-conversion-gate01-151124161555-lva1-app6892/75/ContentMine-Liberating-scholarship-from-Open-publications-and-theses-4-2048.jpg)
![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](https://image.slidesharecdn.com/lille2015-150421041732-conversion-gate01-151124161555-lva1-app6892/75/ContentMine-Liberating-scholarship-from-Open-publications-and-theses-5-2048.jpg)
![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](https://image.slidesharecdn.com/lille2015-150421041732-conversion-gate01-151124161555-lva1-app6892/75/ContentMine-Liberating-scholarship-from-Open-publications-and-theses-6-2048.jpg)
![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)](https://image.slidesharecdn.com/lille2015-150421041732-conversion-gate01-151124161555-lva1-app6892/75/ContentMine-Liberating-scholarship-from-Open-publications-and-theses-49-2048.jpg)
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ContentMine: Liberating scholarship from Open publications and theses
The document discusses the challenges and opportunities in creating an open scholarly infrastructure, highlighting the importance of community-driven approaches to research and knowledge sharing. It critiques the closed nature of current scholarly publishing systems and emphasizes the need for a collaborative, open knowledge model that fosters accessibility and reusability of scientific data. Key figures and examples are presented to illustrate the potential for open science initiatives to transform research practices and democratize knowledge distribution.
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ContentMine: Liberating scholarship from Open publications and theses
- 1. Scholarly Infrastructure: Openor 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 becomesclosed 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 StoppedSOPA”: 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 theDigital 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 stunnedrecently 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 mustbuild 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 Coastdeveloped OpenStreetMap to challenge the monopoly of the UK Ordnance Survey
- 11. The Right toRead is the Right to Mine http://contentmine.org
- 12. OUR TEAM @jenny_molloy Ross Mounce @rmounce RichardSmith- 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-SA3.0 Daily Stream of 100,000 Open Facts Twitter?Indexed by CAT http://catalogue.cottagelabs.com/browsehttp://catalogue.cottagelabs.com/graph
- 14. Content-Mining (TDM*) • NowCOMPLETELY 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=PDFCC-BY SECTIONS MAPS TABLES CHEMISTRY TEXT MATH contentmine.org tackles these
- 16. “nuggets” in ascientific paper quantity units Value ranges Humans aren’t designed to mine this … chemical project places
- 17. What is “Content”? EmilySena (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 theweb 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 RepositoriesDOC 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.
- 21.
- 22. Retrieval/Extraction Technologies • BagOf 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 Thesesfrom HAL repository
- 24.
- 25. Regex for ClinicalTrials
- 26. CLINICAL TRIALS How towe 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 machinereads a chemical thesis nodes are compounds; arrows are reactions
- 28. Natural Language Processing Partof speech tagging (Wordnet, Brown Corpus, etc.)
- 29.
- 30.
- 31. Automatic semantic markupof chemistry Could be used for analytical, crystallization, etc.
- 32. Open Content Miningof 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 reactionscheme, 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 visionin 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 Taeniopygiaguttata 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.
- 38. https://blogs.ch.cam.ac.uk/pmr/2014/06/25/content-mining-we-can-now- mine-images-of-phylogenetic-trees-and-more/ for storyof extraction Thinning Topology Serialization Newick
- 39. Problems • Cannot dohandwriting • 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 onOpen 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, PantonFellow, Training PhD Students
- 43. “Do you thinkyou 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) Phase1: 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.
- 46. TOOLS Open Notebook Science Open engineered repository World community INSTRUMENT validate merge MODEL CODE DATA DATA knowledge calibrate Problemsare 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 OpenEvents • 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 unprecedentedpublic 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 andFellows
Editor's Notes
- #2 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.
- #13 Because information is structured (some examples listed), we can aggregate similar objects and mine using a modular systematic approach.
- #27 Because information is structured (some examples listed), we can aggregate similar objects and mine using a modular systematic approach.