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Principles and practice of Open Science

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Principles and practice of Open Science

  1. 1. Open Science Peter Murray-Rust, ContentMine.org, and University of Cambridge Opencon2015, Bologna, IT 2015-11-18 What is “Open”? Why is it essential? Open Data Content Mining – a battle we must win Young researchers are the present (Mike Eisen)
  2. 2. The Right to Read is the Right to Mine**PeterMurray-Rust, 2011 http://contentmine.org
  3. 3. My European Heroes Young People(ContentMine) NEELIE KROES
  4. 4. Messages • The system is completely broken • We are at war with major publishers • Students have the power to change the world • Universities need help from students • Open is a state of mind • The opposite of Open is broken [1] • Friction destroys Open • Don’t buy it, build it … • … TOGETHER [1] (John Wilbanks)
  5. 5. @Senficon (Julia Reda) :Text & Data mining in times of #copyright maximalism: "Elsevier stopped me doing my research" http://onsnetwork.org/chartgerink/2015/11/16/elsevi er-stopped-me-doing-my-research/ … #opencon #TDM Breaking news: Elsevier stopped me doing my research Chris Hartgerink
  6. 6. 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
  7. 7. http://chemicaltagger.ch.cam.ac.uk/ • Typical Typical chemical synthesis
  8. 8. 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.
  9. 9. C) What’s the problem with this spectrum? Org. Lett., 2011, 13 (15), pp 4084–4087 Original thanks to ChemBark
  10. 10. After AMI2 processing….. … AMI2 has detected a square
  11. 11. 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
  12. 12. Stand back! I am about to do ContentMining! • Erriquez Daniela, Esame finale: Bologna, Aprile 2014 • Dott.ssa Elena Fiorentini, n. 0000274966, TESI DI DOTTORATO, Bologna • Qian Gou, Esame finale: Bologna, finale 2014 • Maurizio BARONTINI, UNIVERSITÀ DEGLI STUDI DELLA TUSCIA DI VITERBO • Terracciano Mario, Esame finale anno 2014
  13. 13. Refs: Erriquez_Daniela_tesi, Fiorentina_Elena_tesi, Gou_Qian_Tesi, mbarontini_tesid, terracciano_maria_tesi BagOfWords for Italian Theses
  14. 14. Copyright and Mining • UK (“Hargreaves”) 2014 legislation: – “personal” “non-commercial*” “research” “data analytics” – legitimizes copying (?to disk), but not publishing • PMR-premise: You cannot do reproducible scientific mining and avoid violating copyright.
  15. 15. Massive political activity in Europe REDA Publisher-influenced
  16. 16. Elsevier wants to control Open Data [asked by Michelle Brook]
  17. 17. Scholarly infrastructure becomes closed No accountability for monitoring and control
  18. 18. 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
  19. 19. [1] The Military-Industrial-Academic complex (1961) (Dwight D Eisenhower, US President) Publishers Academia Glory+? $$, MS review Taxpayer Student Researcher $$ $$ in-kind The Publisher-Academic complex[1]
  20. 20. [Wikipedia:] On the steps of Sproul Hall [Student] Mario Savio gave a famous speech ... But we're a bunch of raw materials that don't mean … to end up being bought by some clients of the University, be they the government, be they industry, be they organized labor, be they anyone! We're human beings! ... There's a time when the operation of the machine becomes so odious — makes you so sick at heart — that you can't take part. You can't even passively take part. And you've got to put your bodies upon the gears and upon the wheels, upon the levers, upon all the apparatus, and you've got to make it stop. And you've got to indicate to the people who run it, to the people who own it, that unless you're free, the machine will be prevented from working at all. [1] Univ California, Berkeley 1964 The Free Speech Movement
  21. 21. 1970’s UK, student occupations and sit-ins University of Stirling Used without permission but with thanks and Love Liverpool , Warwick, Emmanuel Coll Camb., UCL, Glasgow, Middlesex, …
  22. 22. Flower Power 1967 Berkeley 2010 “Flowerpoint”
  23. 23. ["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
  24. 24. Rules for Revolutionaries • Be publicly clear about your public aims. • Gather whole-hearted allies. • Choose your moment/s carefully. • Be prominent – blogs, talks, papers. • Be bold – and probably brave. • Write Liberation Software. • Create slogans, warcries, mantras.
  25. 25. Take the fight to publishers. Hold them accountable for the near- criminal business models they operate on, and the stranglehold they have had on academia for too long. Extending this, I need your help. I want to know if we initiate a formal investigation into the practices of publishers, in terms of the fact that they operate within an unregulated market and enjoy enormous profits to commit immoral acts (creating knowledge inequality). …. I want to know what we can do, and if such an investigation is even feasible, and whether or not we have a legal case supporting us. Don’t sacrifice your career.. [PMR] said it best, that for any revolution blood will be spilled. If you’re making someone angry, you’re probably doing it right. But when you’re ‘advocating’ for open access, maintain one simple rule: don’t be a dick…. (and lots more) Jon Tennant 2014-11-25 http://blogs.egu.eu/palaeoblog/2014/11/25/open-access-wins-all-of- the-arguments-all-of-the-time/
  26. 26. The Right to Read is The Right to Roam The Right to Mine Kinder Mass Trespass used without permission but with love and thanks
  27. 27. How can we achieve Freedom? • Change the law to allow ContentMining – Hard, tedious, but necessary – Requires evidence, campaigning, making yourselves a pain in the arse… • Make all outputs Open – Requires culture change in researchers – Tools: Open Notebook Science, Github, Open source, Social media. – Needs support from funders, learned societies, universities
  28. 28. Four Freedoms (Richard Stallman) The freedom to: 0 run the program as you wish, for any purpose 1 study how the program works, and change it 2 to redistribute copies 3 distribute copies of your modified program Most other “Opens” follow these principles, including CC-BY material. However “Green Open Access” is incompatible with Freedom2 and 3
  29. 29. The Open Definition “Open means anyone can freely access, use, modify, and share for any purpose (subject, at most, to requirements that preserve provenance and openness).”
  30. 30. 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)
  31. 31. Panton Principles for Open Data in science(2010) • PUBLISH YOUR DATA OPENLY • …make an explicit and robust statement of your wishes. • Use a recognized waiver or license that is appropriate for data. • open as defined by the Open Knowledge/Data Definition (… NOT non-commercial) • Explicit dedication of data … into the public domain via PDDL or CCZero Peter Murray-Rust, Cameron Neylon, Rufus Pollock, John Wilbanks
  32. 32. Panton Authors and Fellows
  33. 33. Bjorn Brembs enhanced by OpenData http://bjoern.brembs.net/2015/11/dont-be-afraid-of-open-data/ This is a response to Dorothy Bishop’s post “Who’s afraid of open data?“. After we had published a paper on how Drosophila strains that are referred to by the same name in the literature (Canton S), but came from different laboratories behaved completely different in a particular behavioral experiment, Casey Bergman from Manchester contacted me, asking if we shouldn’t sequence the genomes of these five fly strains to find out how they differ. So I went and behaviorally tested each of the strains again, extracted the DNA from the 100 individuals I had just tested and sent the material to him. I also published the behavioral data immediately on our GitHub project page. Casey then sequenced the strains and made the sequences available, as well. A few weeks later, both Casey and I were contacted by Nelson Lau at Brandeis, showing us his bioinformatics analyses of our genome data. Importantly, his analyses wasn’t even close to what we had planned. On the contrary, he had looked at something I (not being a bioinformatician) would have considered orthogonal (Casey may disagree). So there we had a large chunk of work we would have never done on the data we hadn’t even started analyzing, yet. I was so thrilled! I learned so much from Nelson’s work, this was fantastic! Nelson even asked us to be co-author, to which I quickly protested and suggested, if anything, I might be mentioned in the acknowledgments for “technical assistance” – after all, I had only extracted the DNA. However, after some back-and-forth, he persuaded me with the argument that he wanted to have us as co-authors to set an example. He wanted to show everyone that sharing data is something that can bring you direct rewards in publications. He wanted us to be co-authors as a reward for posting our data and as incentive for others to let go of their fears and also post their data online.
  34. 34. Arguments for Open • Open Science: – is Better Science – can reach and involve everyone – Open Science moves more quickly – Open Science challenges injustice – helps the world It also happens to: – Promote the careers of scientists – Save money
  35. 35. Jean-Claude Bradley Jean-Claude Bradley was one of the most influential open scientists of our time. He was an innovator in all that he did, from Open Education to bleeding edge Open Science; in 2006, he coined the phrase Open Notebook Science. His loss is felt deeply by friends and colleagues around the world. On Monday July 14, 2014 we shall gather at Cambridge University to honour his memory and the legacy he leaves behind with a highly distinguished set of invited speakers to revisit and build upon the ideas which inspired and defined his life’s work. Wikipedia CC BY-SA
  36. 36. Traditional Research and Publication “Lab” work paper/th esis Write rewrite Re-experiment publish ??? Validation?? DATA output “belongs” to publisher process “belongs” to publisher Walls of academia
  37. 37. Free/Open Software Development CODE 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 BORN-OPEN-SOURCE NO WALLS
  38. 38. TOOLS Open Notebook Science Open engineered repository World community INSTRUMENT validate merge MODEL CODE DATA DATA knowledge calibrate Problems are solved communally; Nothing is needlessly duplicated; “publication“ is continuous Machines and humans Working together CC-BY
  39. 39. Mat Todd (Sydney) and MANY collaborators http://opensourcemalaria.org/ (Chrome)
  40. 40. University of Southampton, BSD-like Open
  41. 41. Open Source and Open Data www.crystallography.net
  42. 42. OPEN CLOSED Zenodo Figshare Git Dat OpenOffice Word, PPT LabTrove, cheminfo.org Chemdraw CrystallographyOpenDB Cambridge Cryst data Centre WriteLatex / Overleaf ReadCube, Symplectic,
  43. 43. From Wikipedia CC BY-SA Crowdsourcing
  44. 44. Young people Jenny Molloy Ross Mounce Sam Moore Peter Kraker Rosie GraySophie Kay Sophie: 3rd yr Grad students train 1st year students PANTON ARMS Panton Fellows
  45. 45. Sophie Kershaw, Panton Fellow, Training PhD Students
  46. 46. 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
  47. 47. “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
  48. 48. 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
  49. 49. More Thoughts • Don’t negotiate with walled gardens, make them change or make them obsolete • Building on top of non-Open is very fragile, unpredictable and usually bad engineering
  50. 50. Protecting innovation • Many start-ups get acquired and lose their mission • “Embrace, extend, exterminate” (Microsoft) • Consider adding “Open Lock” clauses to articles of incorporation

Hinweis der Redaktion

  • 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.
  • ChemBark