Wikipedia as an engine for scientific communication andcollaboration at massive scale              Andrew Su, Ph.D.       ...
2The biomedical literature is growing rapidly                       Number of PubMed-indexed articles          1,000,000  ...
3The biomedical literature is growing rapidly                    Average of articlesof humantypical scientist             ...
4High-throughput molecular profiling is powerful                                       Testable                           ...
Filtering, extracting, and summarizing PubMedDocuments Concepts             Review article
Filtering, extracting, and summarizing PubMedDocuments Concepts
7 10k gene “stubs” within Wikipedia ≈ “Gene Wiki”                                         Protein structure         Gene  ...
8 Gene Wiki has a critical mass of readers           Rank 1001-1010: Specialists                               Rank 101-11...
9 Gene Wiki has a critical mass of readersHuss, PLoS Biol, 2008; Huss, NAR, 2010; Good, NAR, 2011
10 Gene Wiki has a critical mass of editors                            Editor count   Editors                             ...
11A review article for every gene is powerful     Reelin: 98 editors, 703 edits since July 2002                           ...
12 The Gene Wiki is timely and current                                               Manny Ramirez                        ...
13 The Gene Wiki is (reasonably) reliable                                      Per edit     Average      Probability      ...
14 Making the Gene Wiki more reliable  Novartis is a multinational   2       The company name is derived  pharmaceutical c...
15 Making the Gene Wiki more reliable  Novartis is a multinational             2         The company name is derived  phar...
16Partnering with traditional scientific publishing
17Partnering with traditional scientific publishing
18Partnering with traditional scientific publishing
19       Collaborators                                                      Group membersDoug Howe, ZFIN                  ...
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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.

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

  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)

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