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Wikipedia as an engine for scientific communication and collaboration at massive scale

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Talk given at Science Writers 2012 in Raleigh, NC on October 27, 2012.

Talk given at Science Writers 2012 in Raleigh, NC on October 27, 2012.


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  • next gen sequencing identifies candidate genesAlso Microarray data, proteomics, GWAS, methylation, post-translational modifications, translocation detection, etc.What do these genes do?
  • Relying on the entire community of scientists to digest the biomedical literature: identification filtering extraction summarization
  • Relying on the entire community of scientists to digest the biomedical literature: identification filtering extraction summarization
  • Reverted four minutes later
  • Reverted four minutes later
  • Transcript

    • 1. Wikipedia as an engine for scientific communication andcollaboration at massive scale Andrew Su, Ph.D. @andrewsu asu@scripps.edu http://sulab.org OK ScienceWriters2012 OK October 27, 2012
    • 2. 2The biomedical literature is growing rapidly Number of PubMed-indexed articles 1,000,000 800,000 600,000 400,000 200,000 0 1979 1984 1989 1994 1999 2004 2009
    • 3. 3The biomedical literature is growing rapidly Average of articlesof humantypical scientist Number capacity read by scientist 20 10 0 1979 1984 1989 1994 1999 2004 2009
    • 4. 4High-throughput molecular profiling is powerful Testable hypothesis ~20,000 genes 100+ candidates 10+ experiments
    • 5. Filtering, extracting, and summarizing PubMedDocuments Concepts Review article
    • 6. Filtering, extracting, and summarizing PubMedDocuments Concepts
    • 7. 7 10k gene “stubs” within Wikipedia ≈ “Gene Wiki” Protein structure Gene summary Symbols and identifiers Gene Ontology annotations Protein interactions Tissue expression Linked pattern references Links to structured databasesHuss, PLoS Biol, 2008
    • 8. 8 Gene Wiki has a critical mass of readers Rank 1001-1010: Specialists Rank 101-110: Scientists CSDA Tau protein CNTNAP2 Interleukin 10 IGSF8 APC Adenosine A3 receptor C-Met RYR1 Factor V ETV6 Interleukin 8 Small heterodimer partner CD44 5-HT1D receptor Histamine H1 receptor TRPC6 Kappa Opioid receptor Interleukin-6 receptor Dihydrofolate reductase Rank 1-10: Laypeople Total: 4.0 million views / month Insulin Titin Human chorionic gonadotropin Vasopressin ANKH CLOCK Catalase Erythropoietin Glucagon Parathyroid hormoneHuss, PLoS Biol, 2008; Huss, NAR, 2010; Good, NAR, 2011
    • 9. 9 Gene Wiki has a critical mass of readersHuss, PLoS Biol, 2008; Huss, NAR, 2010; Good, NAR, 2011
    • 10. 10 Gene Wiki has a critical mass of editors Editor count Editors Edit count Edits Increase of ~10,000 words / month from >1,000 edits Currently 1.42 million words Approximately equal to 230 full-length articlesHuss, NAR, 2010; Good, NAR, 2011
    • 11. 11A review article for every gene is powerful Reelin: 98 editors, 703 edits since July 2002 Hyperlinks to related concepts Heparin: 358 editors, 654 edits since June 2003 AMPK: 109 editors, 203 edits since March 2004 RNAi: 394 editors, 994 edits since October 2002 References to the literature
    • 12. 12 The Gene Wiki is timely and current Manny Ramirez suspended for doping Catalase linked to premature gray hair Also, MGAT2 (obesity), ALDH2 (heart attack), SOX21 (hair loss), SATB1 (breast cancer), TSLP (asthma), CCR5 (HIV), …Huss, NAR, 2010
    • 13. 13 The Gene Wiki is (reasonably) reliable Per edit Average Probability probability lifetime by time Cumulative edits Good edits 98.9% 115.4 d 99.968% Vandalism 1.1% 3.4 d 0.032% Date (0.63% for WP overall)Good, NAR, 2011
    • 14. 14 Making the Gene Wiki more reliable Novartis is a multinational 2 The company name is derived pharmaceutical company from old Greek, and means based in Basel, Switzerland "destroyer of birds".that manufactures drugs such as clozapine (Clozaril), diclofenac (Voltaren), … 2Good, NAR, 2011 http://www.wikitrust.net/
    • 15. 15 Making the Gene Wiki more reliable Novartis is a multinational 2 The company name is derived pharmaceutical company from old Greek, and means based in Basel, Switzerland "destroyer of birds".that manufactures drugs such as clozapine (Clozaril), diclofenac (Voltaren), … 36211 total edits 36 total edits * * * * * * * * * * * * * * High-trust author Low-trust authorGood, NAR, 2011 http://www.wikitrust.net/
    • 16. 16Partnering with traditional scientific publishing
    • 17. 17Partnering with traditional scientific publishing
    • 18. 18Partnering with traditional scientific publishing
    • 19. 19 Collaborators Group membersDoug Howe, ZFIN Ben Good Max NanisJohn Hogenesch, U PennJon Huss, GNF Salvatore Loguercio Chunlei WuLuca de Alfaro, UCSC Ian MacleodAngel Pizzaro, U PennFaramarz Valafar, SDSUPierre Lindenbaum, Fondation Jean DaussetMichael Martone, RushKonrad Koehler, Karo BioWarren Kibbe, Simon Lim, Northwestern http://slideshare.com/andrewsuMany Wikipedia editors WP:MCB Project Contact http://sulab.org asu@scripps.edu @andrewsu +Andrew Su Funding and Support (BioGPS: GM83924, Gene Wiki: GM089820)