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ContentMine: Mining the Scientific Literature


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In a meeting run by OSC at Cambridge 2017-07-12 I present the current capabilities of This includes advocacy, tools and community.

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ContentMine: Mining the Scientific Literature

  1. 1. OSC, University of Cambridge, Cambridge, UK, 2017-07-12 ContentMine: Mining Scientific Literature Peter Murray-Rust TheContentMine Changing the law is not enough. The government, universities and libraries have to actively support researchers.
  2. 2. (2x digital music industry!) ContentMine is an OpenLocked Non-Profit company
  3. 3. (2x digital music industry!) ContentMine is an OpenLocked Non-Profit company Mining 100 million facts from the scientific literature
  4. 4. Topics • Advocacy/Politics. Be engaged or be part of the problem. Assert our rights. • Tools and resources. Demos! We have created a Open toolkit and we welcome help. • Community, especially young people. OpenConCam “Bullied into bad science”. Challenge the Publisher-Academic Complex Slides at
  5. 5. National UK support for TDM since Hargreaves 2014? TDM is effectively controlled by publishers who bully researchers by cutting off subscriptions.
  6. 6. Example: Content Mining can save lives • Search for papers with “Ebola” and “Liberia”
  7. 7. 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. 8. What is “Content”? 03&representation=PDF CC-BY SECTIONS MAPS TABLES CHEMISTRY TEXT MATH tackles these
  9. 9. Examples • Bag of words • Chemistry • Zika • Phylogenetics
  10. 10. Bag of Words Theses from HAL repository Full text is essential
  11. 11. “… simulated by 21cmFAST is in principle independent” “it is a feature of the 21cmFAST code, and is explained in §3.1.” SciCodes[1]: Searching for software in arXiv[1] [1] Proposal to LJ Arnold Foundation (Alice Allen ASCL and PMR) Using the semi-numerical simulation, 21cmFAST, [2] the physics/maths/astronomy.. Preprint server The language identifies the software! arxIv has >500 mentions of “21cmFast”
  12. 12. • Typical Typical chemical synthesis
  13. 13. Automatic semantic markup of chemistry Could be used for analytical, crystallization, etc.
  14. 14. Infrastrucure • ContentMine has built much of this • Interoperates with SciPy, R-OpenSci, GitHub … • Fully Open (CC BY, Apache 2) (20+ repositories)
  15. 15. • 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 • Link to WIKIDATA • Automate daily process (CANARY) Infrastructure
  16. 16. 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
  17. 17. Evolutionary (phylogenetic) trees • International Journal Systematic and Evolutionary Microbiology • Diagrams from 4300 independent articles A machine-compiled microbial supertree from figure-mining thousands of papers Ross Mounce, Peter Murray-Rust, Matthew A Wills Research Ideas and Outcomes 3: e13589 (09 May 2017)
  18. 18. “Root”
  19. 19. 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); Semantic re-usable/computable output (ca 4 secs/image)
  20. 20. Supertree created from 4300 papers
  21. 21. Search for 200 articles with “Zika” file:///Users/pm286/workspace/projects/zika/full.dataTables.html 8 facets linked to Wikidata
  22. 22. ContentMine believes in young people
  23. 23. ContentMine Workshops on Mining Chris Kittel, CM, atMozfest 2015 Stefan Kasberger, CM
  24. 24. 6 ContentMine Fellows for 6 months
  25. 25. Neo Christopher Chung  Warsaw, Computational Biology  Wants to find out geographic and temporal differences in the use of genomic software tools
  26. 26. Paola Masuzzo  Ghent, Computational Omics and Systems Biology  Wants to mine literature around cell migrations and invasion to create 1) collection of minimum requirements, 2) check for nomenclatura consistency and 3) construct a knowledge map
  27. 27. Alexandra Bannach-Brown  Edinburgh, Neuroscience  Problem: huge body of works in animal studies about depressions. systematic review is the main approach for getting insight.  Wants: identify papers in systematic review of depressive behaviour in animals. What drugs, what methods, what outcomes and signs/phenotypes. Use outcomes for document clustering.  and expedite scientific advances."  Corpus: 70.000 Papers
  28. 28. Alexandre Hannud Abdo  “Our goal is to mine facts from global health research and provide automated referenced summaries to practitioners and agents who don’t have the means or the time to navigate the literature.  From Brazil, Life Sciences, works on project about evolution of oncology  extract facts from cancer research conference papers and global health papers OPEN NOTEBOOK RESEARCH
  29. 29. Guanyang Zhang  Biology, Arizona  „My ContentMine Fellowship project will focus on mining weevil-plant associations from literature records.“  „Motivation. Comprising ~70,000 described and 220,000 estimated species, weevils (Curculionoidea) are one of the most diverse plant-feeding insect lineages and constitute nearly 5% of all known animals.“  „Knowledge of host plant associations is critical for pest management, conservation, and comparative biological research. This knowledge is, however, scattered in 300 years of historical literature and difficult to access.“  Weevil-plant association network graph made with Google Fusion Table. Each blue circle is a weevil tribe and yellow circle a plant genus. The size of a circle represents the number of associations.
  30. 30. Lars Willighagen  15 years old NL  Wants: extract data about conifers (relations to chemicals, height etc.)  Outcome: database with webpage containing conifer properties  Table Facts Visualiser DEMO  Card DEMO  Word Cloud  „ I applied to this fellowship to learn new things and combine the ContentMine with two previous projects I never got to finish, and I got really excited by the idea and the ContentMine at large.“
  31. 31. • Chris Hartgerink Tilburg University (NL) • Reproducible Science • Extracting statistical information • Helping authors check reported results • Detecting problematic study results (e.g., clinical trials)
  32. 32. [1] [1] STATCHECK from Chris Hartgerink
  33. 33. “Symmetry [is] indication of potential publication bias” Machines are BETTER than humans here Can we believe meta-analyses of clinical trials?
  34. 34. file:///Users/pm286/workspace/svg2xml/targe t/table/ada2PH1Total.html ContentMine converts PDF to HTML Perfect for machines! PDF table  HTML5 table Horrible for machines! Project with Prof James Thomas, Alison O’Mara-Eves at UCL
  35. 35. And now the main problem…
  36. 36. @Senficon (Julia Reda) :Text & Data mining in times of #copyright maximalism: "Elsevier stopped me doing my research" er-stopped-me-doing-my-research/ … #opencon #TDM Elsevier stopped me doing my research Chris Hartgerink
  37. 37. I am a statistician interested in detecting potentially problematic research such as data fabrication, which results in unreliable findings and can harm policy-making, confound funding decisions, and hampers research progress. To this end, I am content mining results reported in the psychology literature. Content mining the literature is a valuable avenue of investigating research questions with innovative methods. For example, our research group has written an automated program to mine research papers for errors in the reported results and found that 1/8 papers (of 30,000) contains at least one result that could directly influence the substantive conclusion [1]. In new research, I am trying to extract test results, figures, tables, and other information reported in papers throughout the majority of the psychology literature. As such, I need the research papers published in psychology that I can mine for these data. To this end, I started ‘bulk’ downloading research papers from, for instance, Sciencedirect. I was doing this for scholarly purposes and took into account potential server load by limiting the amount of papers I downloaded per minute to 9. I had no intention to redistribute the downloaded materials, had legal access to them because my university pays a subscription, and I only wanted to extract facts from these papers. Full disclosure, I downloaded approximately 30GB of data from Sciencedirect in approximately 10 days. This boils down to a server load of 0.0021GB/[min], 0.125GB/h, 3GB/day. Approximately two weeks after I started downloading psychology research papers, Elsevier notified my university that this was a violation of the access contract, that this could be considered stealing of content, and that they wanted it to stop. My librarian explicitly instructed me to stop downloading (which I did immediately), otherwise Elsevier would cut all access to Sciencedirect for my university. I am now not able to mine a substantial part of the literature, and because of this Elsevier is directly hampering me in my research. [1] Nuijten, M. B., Hartgerink, C. H. J., van Assen, M. A. L. M., Epskamp, S., & Wicherts, J. M. (2015). The prevalence of statistical reporting errors in psychology (1985–2013). Behavior Research Methods, 1–22. doi: 10.3758/s13428-015-0664-2 Chris Hartgerink’s blog post
  38. 38. Wiley also stopped me (Chris Hartgerink) doing my research In November, I wrote about how Elsevier wanted me to stop downloading scientific articles for my research. Today, Wiley also ordered me to stop downloading. As a quick recapitulation: I am a statistician doing research into detecting potentially problematic research such as data fabrication and estimating how often it occurs. For this, I need to download many scientific articles, because my research applies content mining methods that extract facts from them (e.g., test statistics). These facts serve as my data to answer my research questions. If I cannot download these research articles, I cannot collect the data I need to do my research. I was downloading psychology research articles from the Wiley library, with a maximum of 5 per minute. I did this using the tool quickscrape, developed by the ContentMine organization. With this, I have downloaded approximately 18,680 research articles from the Wiley library, which I was downloading solely for research purposes. Wiley noticed my downloading and notified my university library that they detected a compromised proxy, which they had immediately restricted. They called it “illegally downloading copyrighted content licensed by your institution”. However, at no point was there any investigation into whether my user credentials were actually compromised (they were not). Whether I had legitimate reasons to download these articles was never discussed. The original email from Wiley is available here. As a result of Wiley denying me to download these research articles, I cannot collect data from another one of the big publishers, alongside Elsevier. Wiley is more strict than Elsevier by immediately condemning the downloading as illegal, whereas Elsevier offers an (inadequate) API with additional terms of use (while legitimate access has already been obtained). I am really confused about what the publisher’s stance on content mining is, because Sage and Springer seemingly allow it; I have downloaded 150,210 research articles from Springer and 12,971 from Sage and they never complained about it.
  39. 39. What you must do • ACTIVELY encourage Mining and researchers • INVEST in tools, resources, training • ENCOURAGE cooperative publishers • PROTECT researchers from aggressive publishers • Need ACTIONS, not WORDS or it will be too late
  40. 40. OUP1 Data Mining Policy … we are happy to accommodate TDM for non- commercial use. Although researchers are not required to request permission for non-commercial text-mining, OUP is happy to offer consultation … including avoidance of any technical safeguards triggers OUP has in place 1 Oxford University Press
  41. 41. H2020 project, Coordinated by LIBER Evidence collection
  42. 42. Julia Reda, Pirate MEP, running ContentMine software to liberate science 2016-04-16
  43. 43. • Speak out. Write to your MEP, MP, Vice-chancellor. • Assert RESEARCHER RIGHTS. • Stand up to Publisher-Academic bullies. • Create communities of practice. Young people. • Write Open software Action is required