Content Mining of Science in Cambridge

Content Mining of Science in Cambridge

• 1.
  Content Mining ofScience in Cambridge Peter Murray-Rust, Dept of Chemistry, University of Cambridge libraries@cambridge, Cambridge, UK 2016-01-07 What is mining? Why is it useful? Open Access and UK “Hargreaves” legislation How Cambridge can become a world leader
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  The Right toRead is the Right to Mine**PeterMurray-Rust, 2011 http://contentmine.org
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  Use Cases ofContentMining • Epidemiology of obesity (Cambridge U) • (OKF, OpenTrials) Mapping clinical trials repositories to reports in scientific literature • Mining chemical reactions from patents • Creating a bacterial supertree-of-life from 4500 papers
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  Polly has 20seconds to read this paper… …and 10,000 more
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  ContentMine software cando this in a few minutes Polly: “there were 10,000 abstracts and due to time pressures, we split this between 6 researchers. It took about 2-3 days of work (working only on this) to get through ~1,600 papers each. So, at a minimum this equates to 12 days of full-time work (and would normally be done over several weeks under normal time pressures).”
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  400,000 Clinical Trials In10 government registries Mapping trials => papers http://www.trialsjournal.com/content/16/1/80 2009 => 2015. What’s happened in last 6 years?? Search the whole scientific literature For “2009-0100068-41”
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  ContentMine-ing strategy • Discover.Crawl the COMPLETE relevant literature. => bibliography • Scrape (download). ALL papers • Index papers => Facts • Search/analyze papers => complex science • Extract, Annotate, Aggregate (“Transformative”)
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  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
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  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 CONTENTMINE Complete OPEN Platform for Mining Scientific Literature
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  http://chemicaltagger.ch.cam.ac.uk/ • Typical Typical chemicalsynthesis
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  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.
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  Facts in context dailyIUCN endangered species news en.wikipedia.org CC By-SA
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  ContentMine Fact ofThe Day • Fact of the day • Endangered species in recent science • Facts • Bubbles
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  https://en.wikipedia.org/wiki/Tree_of_life CC BY-SA
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  “Root” 4500 papers each with1 tree
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  OCR (Tesseract) Norma (imageanalysis) (((((Pyramidobacter_piscolens:195,Jonquetella_anthropi:135):86,Synergistes_jonesii:301):131,Thermotoga _maritime:357):12,(Mycobacterium_tuberculosis:223,Bifidobacterium_longum:333):158):10,((Optiutus_te rrae:441,(((Borrelia_burgdorferi:…202):91):22):32,(Proprinogenum_modestus:124,Fusobacterium_nucleat um:167):217):11):9); Semanticre-usable/computable output (ca 4 secs/image)
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  Supertree for 924species Tree
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  Supertree created from4300 papers
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  Copyright and Mining •UK (“Hargreaves”) 2014 legislation: – “personal” “non-commercial*” “research” “data analytics” – legitimizes copying (?to disk), but not publishing *teaching, textbooks, etc. may be “commercial”
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  STM Publishers preventMining • FUD & disinformation about legality (Elsevier) • Monopolies on infrastructure (“API”s, CCC Rightfind) • Technical obstruction (Wiley Captcha, Macmillan Readcube) • Restrictive contracts with libraries (ALL) [1] • Wasting my/our time (ALL) [1] [You may not] utilize the TDM Output to enhance … subject repositories in a way that would [… ] have the potential to substitute and/or replicate any other existing Elsevier products, services and/or solutions.
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  WILEY … “newsecurity feature… to prevent systematic download of content “[limit of] 100 papers per day” “essential security feature … to protect both parties (sic)” CAPTCHA User has to type words
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  ContentMine working withLibraries • Cambridge: Library, Plant Sciences, Public Health, Chemistry • Cochrane Collaboration on Systematic Reviews of Clinical Trials • FutureTDM (H2020, LIBER) • Running workshops and training • We have dedicated servers running in chemistry
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  My European Heroes YoungPeople(ContentMine) NEELIE KROES