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The Content Mine (presented at UKSG)
- 1. The Content Mine PeterMurray-Rust University of Cambridge and Open Knowledge Foundation A community of people and machines to extract 100,000,000 scientific facts from the scholarly literature Slides: CC-BY Images © Wikimedia CC-BY-SA
- 3. If you’re bored… important THREE most important Open Access publishers? (besides BMC and PLoS) THREE most important Open Access repositories?
- 4. TDM* (“Text-and-Data-mining”) isthe use of machines to read and understand massive amounts of documents “The Right to Read is the Right to Mine“. PMR + OKFN “Closed Access means people die” (PM-R) “Text and Data Mining saves Lives “ (John McNaught) *PMR uses “content mining”
- 5. Who’s this? (Credit: SethRosenblatt/CNET)
- 6. Aaron Swartz Died 2012-11-08 Facing30 years in jail for Downloading JStor http://news.cnet.com/8301-13578_357611642-38/call-to-action-kicks-off-secondaaron-swartz-hackathon/ (Credit: Seth Rosenblatt/CNET)
- 7. Typical papers destroydata Numeric: astro1307.5851v4.pdf Diagram: birds1471-2148-11-313.pdf
- 8. RCUK Wellcome ERC NSF … require fully OPEN [atResearch Data Alliance, we are entering a new “era of open science”, which will be “good for citizens, good for scientists and good for society”. She explicitly highlighted the transformative potential of open access, open data, open software and open educational resources – mentioning the EU’s policy requiring open access to all publications and data resulting from EU funded research. http://blog.okfn.org/2013/03/21/we-are-entering-an-era-of-open-science-says-eu-vp-neeliekroes/#sthash.3SWDXDE6.dpuf
- 9. Content Mining • • • • • • Make sciencediscoverable Extract facts for research Build reusable objects Aggregate Create new businesses Check for errors => better science
- 10. Content Mining Problems • • • • Secondarypublishers create walled gardens Publishers’ contracts ban content-mining. Publishers cut off Universities who mine Publishers lobby governments to require “licences for content mining” • UK Hargreaves legislation will override this by law. Starts 2014. http://blogs.ch.cam.ac.uk/pmr/2013/10/02/text-and-data-mining-fighting-for-ourdigital-future-peter-murray-rust-is-the-problem/
- 11. Walled Gardens (“Free”but not “Open”) service provider has control over applications, cont ent, and media and restricts convenient access to non-approved applications or content. Examples: Mendeley, Facebook, Cambridge Crystallographic Data Centre, OCLC #animalgarden “Walled Gardens” https://vimeo.com/34323486
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- 14. Licences destroy ContentMining STM Publishers Licence WE WALKED OUT • Brit Library • JISC • RLUK • OKFN • … • Ross Mounce • PM-R 2012_03_15_Sample_Licence_Text_Data_Mining.pdf (Summary: PMR has NO rights) • *cannot publish to: + “libraries, repositories, or archives” • *cannot+ “Make the results of any TDM Output available on an externally facing server or website” • “Subscriber shall pay a *…+ fee” Heather Piwowar: “negotiating with publishers *made me physically ill+”
- 15. Licensing TDM islike publishers taxing spectacles
- 16. We can’t turna hamburger into a cow But we can now turn PDFs into Science
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- 20. PDF AMI HTML Evolutionof ultraviolet vision in the largest avian radiation - the passerines Anders Ödeen 1* , Olle Håstad 2,3 and Per Alström 4 Styles , superscripts And diåcritics preserved!
- 21. 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
- 22. Typical phylo tree:60 nodes, complex and miniscule annotation, vertical text, hyphenation and valuable branch lengths. AMI extracts ALL
- 23. AMI 0.84 0.91 0.93 0.95 Posterior probability 23.12 34.54 37.21 38.55 NexML HTML AMI can MEASURE Branchlengths! Acanthisitta Acrocephalus Ailuroedus Ailuroedus Amytornis Camptostoma Acanthisittidae Acanthizidae Acrocephalidae Callaeidae Campephagidae Cnemophilidae Corvidae Genus Family
- 24. 10 million spectrapublished /year
- 27. Review of theNMR data reported in the Supporting Information in this article evidences instances where some of the spectra were inappropriately edited to remove impurities. A coauthor and former student, Dr. Bruno Anxionnat, has shared with me formal communication in which he states “I would like to take full responsibility for this entire situation. I was in charge of making the SI of my papers and I erased some peaks without telling anybody. All my supervisors (Pr. Cossy, Dr. Gomez Pardo and Dr. Ricci) trusted me and I wasn't dependable. I am the only one who has to be blamed for all that, in any case them. I know my behavior is highly unethical. I am deeply sorry for what I have done and for hurting people….”
- 28. Crystallography Walled Garden serviceprovider has control over applications, conte nt, and media and restricts convenient access to non-approved applications or content.
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- 30. Crystaleye • A databaseof 200,000 crystal structures scraped from publications CIF supplemental information • CML molecules and name-value pairs • Re-usable as fragment base Nick Day, Jim Downing, Sam Adams, N. W. England and Peter Murray-Rust* J.Appl.Cryst. (2012). 45 , 316– 323, doi:10.1107/S0021889812006462 http://wwmm.ch.cam.ac.uk/crystaleye
- 32. “nuggets” in ascientific paper places project Value ranges quantity units chemical Humans aren’t designed to mine this …
- 33. The Content Mine Acommunity of people and machines to extract scientific facts from the scholarly literature on a global scale. https://vimeo.com/78353557
- 34. AMI 100,000 lines ofOpen code for translating PDFs to science. 10 years work (PMR). AMI works!
- 35. We have friends •ProPublica is a NY digital-democracy newspaper • Tabula is an Open PDF-table extractor • Mozilla fights for web freedom
- 37. Boot-Camps and hacks OpenScience, Oxford 2013-11-27 (sold out before announcement!)
- 38. Collaborators: I have talkedwith: • BMC • PLoS • British Library • Mozilla • Software Carpentry • EuropePMC • Creative Commons • OKFN I hope to talk with: • Wellcome • JISC • Ubiquity • Royal Society • Kitware • SPARC • … • …
- 39. • • • • • “The right toread is the right to mine” Unrestricted TDM saves lives Libraries – reject TDM restrictions Publishers – Damascene conversion Funders – insist on CC-BY @petermurrayrust http://blogs.ch.cam.ac.uk/pmr
- 41. 3 most importantOpen Access repositories? • Wikimedia • Github, StackOverflow. • National libraries and museums. 3 most important Open Access publishers? • • • • Wikipedia NIH+EBI+OtherBioDatabases arXiv, CERN/SCOAP +PLoS+BMC
- 42. 300 Billion USDannually on Science+Medicine FACTS! LOST! FACTS! LOST! FACTS! LOST! FACTS! • “we repeat about 25% of our chemistry because we didn’t know we’d done it already” • 10,000 phylogenetic trees at 25,000 USD each; only 4% have data (loss = 240 Million USD) • Computational chemistry – materials NO DATA, perhaps 1,000,000,000 USD FACTS! LOST! FACTS! LOST! FACTS! LOST! FACTS!