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Wikis at work A short introduction to 'wikis' and wikis for biology Dan Bolser and Paolo Romano URL for slides: http://
Overview of today's course <ul><li>Session 1  (35 min) : </li></ul><ul><ul><li>What is a wiki?  – A gentle introduction to...
Overview of today's course <ul><li>Session 3  (35 min)‏ </li></ul><ul><ul><li>Semantic MediaWiki   – Software for 'data wi...
 
Session 1
What is a wiki?
Wiki means QUICK!
Wiki is a  quicker  way to let people put content on the web Old way:
Wiki is a quicker way to let people put content on the web Old way:
Wiki is a quicker way to let people put  content  on the web Old way:
Wiki is a quicker way to let people put  content  on the web Old way: <ul><li>Host </li></ul><ul><li>HTML editor </li></ul...
Wiki is a quicker way to let people put  content  on the web Old way:
Wiki is a quicker way to let people put  content  on the web Old way: Wiki way:
Wiki means QUICK!
<ul><li>There is no longer one single 'point of control' for managing web content. </li></ul><ul><li>Content is managed by...
Is this good or bad?
Other advantages of wiki <ul><li>There are many other advantages over 'traditional' web publishing... </li></ul><ul><ul><l...
The rise of the wiki
Condensed history <ul><li>1994: Cunningham coined the term 'wiki'. </li></ul><ul><ul><li>A site (for software developers) ...
 
Wikipedia <ul><li>Size </li></ul><ul><ul><li>Stats. </li></ul></ul><ul><li>Growth‏ </li></ul><ul><ul><li>Research. </li></...
Wikipedia <ul><li>Size </li></ul><ul><ul><li>19.7 million articles </li></ul></ul><ul><ul><ul><li>3.7 million in English <...
Wikipedia <ul><li>Growth (Kittur)‏ </li></ul><ul><ul><li>Wikipedia has been growing exponentially since 2002 (Voss)‏ </li>...
Wikipedia <ul><li>Rules </li></ul><ul><ul><li>Their are no rules! </li></ul></ul><ul><ul><li>The 'five pillars' of Wikiped...
Wikipedia <ul><li>Culture </li></ul><ul><ul><li>Their are no rules! </li></ul></ul><ul><ul><li>The 'five pillars' of Wikip...
Moving on... <ul><li>Is WP, or something like it, the future for science? </li></ul><ul><li>Lets find out in Session 2! </...
Session 1, References <ul><li>http://wikipedia.org/wiki/ History_of_wikis </li></ul><ul><li>http://wikipedia.org/wiki/ Wik...
 
Session 2
Scientific wikis
Community annotation
Annotation
Annotation
Community annotation <ul><li>Driven by two key factors: </li></ul><ul><li>The vast increase in biological data </li></ul><...
BioMoore's Law <ul><li>Over time: </li></ul><ul><ul><li>Cost per unit of information can be decreased by orders of magnitu...
BioMoore's Law <ul><li>Over time: </li></ul><ul><ul><li>Cost per unit of information can be decreased by orders of magnitu...
Community annotation is essential <ul><li>Centralised databases can't cope with annotating the influx of data. </li></ul><...
But Wikipedia isn’t  always the answer ... <ul><li>Wikipedia is an educational resource. </li></ul><ul><ul><li>All article...
BioWikis <ul><li>Wikis with a biological subject matter, customized for analysis, presentation and collection of specific ...
Wikis for biology
Proteopedia <ul><li>http://proteopedia.org/ </li></ul><ul><li>Aim – To make knowledge about proteins accessible. </li></ul...
WikiPathways <ul><li>http://wikipathways.org </li></ul><ul><li>Aim – The curation of biological pathways. </li></ul><ul><l...
EcoliWiki <ul><li>http://ecoliwiki.net/ </li></ul><ul><li>Aim – Share info related to non-pathogenic E. coli. </li></ul><u...
CHDWiki <ul><li>http://goo.gl/info/Zxg8H </li></ul><ul><li>Aim(?) – Geneticists, clinicians, and mol. biologists working o...
SEQwiki <ul><li>http://seqwiki.org </li></ul><ul><li>Aim – a catalogue of analysis tools and, technologies for NGS. </li><...
Listing of biowikis... <ul><li>http://bioinformatics.org/wiki/BioWiki </li></ul>
BioWikis <ul><li>There is a variety of different systems. </li></ul><ul><li>All seek to 'recognize' contributors (biologis...
The MCB Portal in Wikipedia <ul><li>http://en.wikipedia.org/wiki/ Wikipedia:MCB </li></ul><ul><li>Aim – Better organize in...
Gene Wiki <ul><li>http://en.wikipedia.org/wiki/ Portal:Gene_Wiki </li></ul><ul><li>Aim – applying community intelligence t...
Wikis for Cancer?
Some aditional references <ul><li>Fan JB, Chee MS, Gunderson KL. Highly parallel genomic assays. Nature reviews. Genetics ...
 
Session 3
Semantic MediaWiki
Semantic MediaWiki (a data wiki engine)‏ <ul><li>What is SMW? </li></ul><ul><li>Motivation </li></ul><ul><li>Frontend </li...
References <ul><li>SMW Homepage: http://semantic-mediawiki.org </li></ul><ul><li>MW Templates: http://www.mediawiki.org/wi...
Cell Lines Wiki
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Transcript of "Wikis at work"

  1. 1. Wikis at work A short introduction to 'wikis' and wikis for biology Dan Bolser and Paolo Romano URL for slides: http://
  2. 2. Overview of today's course <ul><li>Session 1 (35 min) : </li></ul><ul><ul><li>What is a wiki? – A gentle introduction to the wiki concept, and a look at Wikipedia. </li></ul></ul><ul><li>Session 2 (35 min)‏ </li></ul><ul><ul><li>Biological wikis! – A review of some of the most important wikis for biology (BioWikis). </li></ul></ul><ul><li>BREAK (15 min)‏ </li></ul>
  3. 3. Overview of today's course <ul><li>Session 3 (35 min)‏ </li></ul><ul><ul><li>Semantic MediaWiki – Software for 'data wikis'. </li></ul></ul><ul><ul><li>Cell Lines Wiki – A pilot scientific wiki. </li></ul></ul><ul><li>Practical session (60 min)‏ </li></ul><ul><ul><li>Editing Wikipedia (for the first time?)‏ </li></ul></ul><ul><ul><li>Working with Cell lines Wiki – A gentle introduction to some of the key features. </li></ul></ul>
  4. 5. Session 1
  5. 6. What is a wiki?
  6. 7. Wiki means QUICK!
  7. 8. Wiki is a quicker way to let people put content on the web Old way:
  8. 9. Wiki is a quicker way to let people put content on the web Old way:
  9. 10. Wiki is a quicker way to let people put content on the web Old way:
  10. 11. Wiki is a quicker way to let people put content on the web Old way: <ul><li>Host </li></ul><ul><li>HTML editor </li></ul><ul><li>FTP software </li></ul><ul><li>Domain name </li></ul>
  11. 12. Wiki is a quicker way to let people put content on the web Old way:
  12. 13. Wiki is a quicker way to let people put content on the web Old way: Wiki way:
  13. 14. Wiki means QUICK!
  14. 15. <ul><li>There is no longer one single 'point of control' for managing web content. </li></ul><ul><li>Content is managed by a decentralized community of participating users. </li></ul>Wiki is radically different!
  15. 16. Is this good or bad?
  16. 17. Other advantages of wiki <ul><li>There are many other advantages over 'traditional' web publishing... </li></ul><ul><ul><li>Notification of changes </li></ul></ul><ul><ul><li>History of changes </li></ul></ul><ul><ul><li>Discussion of changes </li></ul></ul>
  17. 18. The rise of the wiki
  18. 19. Condensed history <ul><li>1994: Cunningham coined the term 'wiki'. </li></ul><ul><ul><li>A site (for software developers) with pages that can be edited via the browser, each with a page history. </li></ul></ul><ul><li>Over the next five years it spawned alternative wiki applications and websites (wiki culture). </li></ul><ul><ul><li>By 2000, it had developed lots of of spin-off content, most notably MeatballWiki (for general discussion). </li></ul></ul><ul><li>2001, Wikipedia launched. </li></ul><ul><li>2007, Wikipedia in the worlds top 10 web sites. </li></ul>
  19. 21. Wikipedia <ul><li>Size </li></ul><ul><ul><li>Stats. </li></ul></ul><ul><li>Growth‏ </li></ul><ul><ul><li>Research. </li></ul></ul><ul><li>Rules </li></ul><ul><ul><li>e.g. Deleting content. </li></ul></ul><ul><li>Culture </li></ul><ul><ul><li>e.g. Anatomy of a talk page. </li></ul></ul>Almost all of its articles can be edited by anyone with access to the site, and it has about 90,000 regularly active contributors.
  20. 22. Wikipedia <ul><li>Size </li></ul><ul><ul><li>19.7 million articles </li></ul></ul><ul><ul><ul><li>3.7 million in English </li></ul></ul></ul><ul><ul><ul><li>847,069 in Italian (4 th out of 282)‏ </li></ul></ul></ul><ul><ul><li>2.7 billion monthly hits from the US alone. </li></ul></ul><ul><ul><li>7 th most popular site in the world. </li></ul></ul><ul><ul><li>The largest and most popular general reference work. </li></ul></ul>
  21. 23. Wikipedia <ul><li>Growth (Kittur)‏ </li></ul><ul><ul><li>Wikipedia has been growing exponentially since 2002 (Voss)‏ </li></ul></ul><ul><ul><li>“ wisdom of crowds” or “elite users” </li></ul></ul><ul><ul><ul><li>a large number of people with a small number of edits, or </li></ul></ul></ul><ul><ul><ul><li>a core group who do most of the work? </li></ul></ul></ul>
  22. 24. Wikipedia <ul><li>Rules </li></ul><ul><ul><li>Their are no rules! </li></ul></ul><ul><ul><li>The 'five pillars' of Wikipedia' </li></ul></ul><ul><ul><li>Standard deletion procedure... </li></ul></ul>
  23. 25. Wikipedia <ul><li>Culture </li></ul><ul><ul><li>Their are no rules! </li></ul></ul><ul><ul><li>The 'five pillars' of Wikipedia' </li></ul></ul><ul><ul><li>Discussion! </li></ul></ul><ul><ul><ul><li>(Not bureaucracy)‏ </li></ul></ul></ul>
  24. 26. Moving on... <ul><li>Is WP, or something like it, the future for science? </li></ul><ul><li>Lets find out in Session 2! </li></ul>
  25. 27. Session 1, References <ul><li>http://wikipedia.org/wiki/ History_of_wikis </li></ul><ul><li>http://wikipedia.org/wiki/ Wikipedia </li></ul><ul><li>Voss, J. Measuring Wikipedia. In Proceedings of the ISSI 2005 (Stockholm, Sweden, July 24-28, 2005). </li></ul><ul><li>Kittur A, Chi EH, Pendleton BA, Suh B, Mytkowicz T. Power of the few vs. wisdom of the crowd: Wikipedia and the rise of the bourgeoisie. CHI 2007. </li></ul><ul><li>http://wikipedia.org/wiki/ Wikipedia:Five_pillars </li></ul><ul><li>http://meta.wikimedia.org/wiki/ Research: Newsletter/2011-07-25 </li></ul>
  26. 29. Session 2
  27. 30. Scientific wikis
  28. 31. Community annotation
  29. 32. Annotation
  30. 33. Annotation
  31. 34. Community annotation <ul><li>Driven by two key factors: </li></ul><ul><li>The vast increase in biological data </li></ul><ul><li>The clear success of Wikipedia </li></ul>
  32. 35. BioMoore's Law <ul><li>Over time: </li></ul><ul><ul><li>Cost per unit of information can be decreased by orders of magnitude. </li></ul></ul><ul><ul><li>Throughput is increased by orders of magnitude. </li></ul></ul><ul><ul><ul><li>Fan et al. 2006 . Nat Rev Genet . </li></ul></ul></ul><ul><li>Comprehensive disease studies that might require ~1bn genotypes would now cost only a few million dollars. </li></ul><ul><ul><li>Revolution in human genetics. </li></ul></ul>
  33. 36. BioMoore's Law <ul><li>Over time: </li></ul><ul><ul><li>Cost per unit of information can be decreased by orders of magnitude. </li></ul></ul><ul><ul><li>Throughput is increased by orders of magnitude. </li></ul></ul><ul><ul><ul><li>Fan et al. 2006 . Nat Rev Genet . </li></ul></ul></ul><ul><li>Comprehensive disease studies that might require ~1bn genotypes would now cost only a few million dollars. </li></ul><ul><ul><li>Revolution in human genetics. </li></ul></ul>
  34. 37. Community annotation is essential <ul><li>Centralised databases can't cope with annotating the influx of data. </li></ul><ul><li>Less investment in more specialised data. </li></ul><ul><ul><li>Fewer people with a stake. </li></ul></ul><ul><ul><li>Specialists more disparate. </li></ul></ul><ul><ul><ul><li>Communities are smaller and more focused. </li></ul></ul></ul><ul><li>Do wikis hold the answer? </li></ul><ul><ul><li>Wikipedia as a model… </li></ul></ul>
  35. 38. But Wikipedia isn’t always the answer ... <ul><li>Wikipedia is an educational resource. </li></ul><ul><ul><li>All articles are encyclopaedic in style. </li></ul></ul><ul><ul><li>Explicitly forbids data from ‘original research’: </li></ul></ul><ul><ul><ul><li>http://wikipedia.org/wiki/Wikipedia:No_original_research </li></ul></ul></ul><ul><ul><ul><ul><li>“ Wikipedia does not publish original research” . </li></ul></ul></ul></ul><ul><ul><li>No tools for the specific analysis, presentation, or collection of ‘biological’ data. </li></ul></ul><ul><li>BioWikis! </li></ul>
  36. 39. BioWikis <ul><li>Wikis with a biological subject matter, customized for analysis, presentation and collection of specific biological data and biological data types: </li></ul>
  37. 40. Wikis for biology
  38. 41. Proteopedia <ul><li>http://proteopedia.org/ </li></ul><ul><li>Aim – To make knowledge about proteins accessible. </li></ul><ul><li>Features: </li></ul><ul><ul><li>Interactive 3D viz. </li></ul></ul><ul><ul><li>Contributions linked to publications. </li></ul></ul><ul><li>Problems </li></ul><ul><ul><li>Doesn't work on all browsers. </li></ul></ul><ul><ul><li>Can be slow. </li></ul></ul><ul><li>Reference </li></ul><ul><ul><li>Hodis, E. et al., 2008. Proteopedia - a scientific “wiki” bridging the rift between three-dimensional structure and function of biomacromolecules. Genome biology, 9(8), p.R121. </li></ul></ul>
  39. 42. WikiPathways <ul><li>http://wikipathways.org </li></ul><ul><li>Aim – The curation of biological pathways. </li></ul><ul><li>Features: </li></ul><ul><ul><li>Interactive pathway editing. </li></ul></ul><ul><ul><li>Integrated to many biological databases. </li></ul></ul><ul><li>Problems </li></ul><ul><ul><li>Doesn't work on all browsers. </li></ul></ul><ul><ul><li>Can be slow. </li></ul></ul><ul><li>Reference </li></ul><ul><ul><li>Pico, A.R. et al., 2008. WikiPathways: pathway editing for the people. PLoS biology, 6(7), p.e184. </li></ul></ul>
  40. 43. EcoliWiki <ul><li>http://ecoliwiki.net/ </li></ul><ul><li>Aim – Share info related to non-pathogenic E. coli. </li></ul><ul><li>Features: </li></ul><ul><ul><li>Very extensive and well structured domain information. </li></ul></ul><ul><ul><li>Referencing is good. </li></ul></ul><ul><li>Problems </li></ul><ul><ul><li>Big resource </li></ul></ul><ul><ul><li>Specific focus, could it be applied to others? </li></ul></ul><ul><li>Reference </li></ul><ul><ul><li>EcoliWiki, 2007. EcoliHub’s subsystem for community annotation. http://ecoliwiki.net. </li></ul></ul>
  41. 44. CHDWiki <ul><li>http://goo.gl/info/Zxg8H </li></ul><ul><li>Aim(?) – Geneticists, clinicians, and mol. biologists working on Congenital Heart Defects. </li></ul><ul><li>Features: </li></ul><ul><ul><li>Curated gene lists. </li></ul></ul><ul><ul><li>PPI browser. </li></ul></ul><ul><li>Problems </li></ul><ul><ul><li>Very old MediaWiki fork </li></ul></ul><ul><ul><li>Used? </li></ul></ul><ul><li>Reference </li></ul><ul><ul><li>Barriot, R. et al., 2010. Collaboratively charting the gene-to-phenotype network of human congenital heart defects. Genome medicine, 2(3), p.16. </li></ul></ul>
  42. 45. SEQwiki <ul><li>http://seqwiki.org </li></ul><ul><li>Aim – a catalogue of analysis tools and, technologies for NGS. </li></ul><ul><li>Features </li></ul><ul><ul><li>Structured data. </li></ul></ul><ul><ul><li>Linked to an established forum. </li></ul></ul><ul><li>Problems </li></ul><ul><ul><li>Data can become error prone. </li></ul></ul><ul><ul><li>Data is difficult to centrally manage. </li></ul></ul><ul><li>Reference </li></ul><ul><ul><li>Li J.W., et. al. 2012. The SEQanswers wiki: A wiki database of tools for high throughput sequencing analysis. Nucleic Acids Research 2012 Database special issue. </li></ul></ul>
  43. 46. Listing of biowikis... <ul><li>http://bioinformatics.org/wiki/BioWiki </li></ul>
  44. 47. BioWikis <ul><li>There is a variety of different systems. </li></ul><ul><li>All seek to 'recognize' contributors (biologists) in a way more familiar to scientists than Wikipedia. </li></ul><ul><li>Most have features not found in Wikipedia. </li></ul><ul><ul><li>Some projects use the base of Wikipedia to successfully build integrated 'sub-projects'... </li></ul></ul>
  45. 48. The MCB Portal in Wikipedia <ul><li>http://en.wikipedia.org/wiki/ Wikipedia:MCB </li></ul><ul><li>Aim – Better organize information related to molecular and cell biology on Wikipedia. </li></ul><ul><li>Features </li></ul><ul><ul><li>Integrated with WP </li></ul></ul><ul><li>Problems </li></ul><ul><ul><li>The project can be confusing to those unfamiliar with Wikipedia. </li></ul></ul><ul><li>Reference </li></ul><ul><ul><li>... </li></ul></ul>
  46. 49. Gene Wiki <ul><li>http://en.wikipedia.org/wiki/ Portal:Gene_Wiki </li></ul><ul><li>Aim – applying community intelligence to gene annotation. </li></ul><ul><li>Special features: </li></ul><ul><ul><li>Semi-automatic gene curation system. </li></ul></ul><ul><li>Problems </li></ul><ul><ul><li>The project can be confusing to those unfamiliar with Wikipedia. </li></ul></ul><ul><li>Reference </li></ul><ul><ul><li>Huss, J.W. et al., 2008. A gene wiki for community annotation of gene function. PLoS biology, 6(7), p.e175. </li></ul></ul>
  47. 50. Wikis for Cancer?
  48. 51. Some aditional references <ul><li>Fan JB, Chee MS, Gunderson KL. Highly parallel genomic assays. Nature reviews. Genetics 7, 632-44 (2006). </li></ul><ul><li>The Molecular modelling blog post http://rosettadesigngroup.com/blog/373/scientific-wikis-part-i/ </li></ul><ul><li>http://bifx.org/wiki/BioWiki </li></ul><ul><li>Daub, J. et al., 2008. The RNA WikiProject: community annotation of RNA families. RNA (New York, N.Y.), 14(12), pp.2462-4. </li></ul><ul><li>Stehr, H. et al., 2010. PDBWiki: added value through community annotation of the Protein Data Bank. Database, p.baq009-baq009. </li></ul><ul><li>Flórez, L.A. et al., 2009. A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. Database : the journal of biological databases and curation, p.bap012 </li></ul>
  49. 53. Session 3
  50. 54. Semantic MediaWiki
  51. 55. Semantic MediaWiki (a data wiki engine)‏ <ul><li>What is SMW? </li></ul><ul><li>Motivation </li></ul><ul><li>Frontend </li></ul><ul><ul><li>What you see as a user of SMW. </li></ul></ul><ul><li>Backend </li></ul><ul><ul><li>What you do as a SMW site developer... </li></ul></ul><ul><li>Data </li></ul><ul><li>Properties and types </li></ul><ul><li>Classes </li></ul><ul><li>Templates </li></ul><ul><li>Forms </li></ul><ul><li>Queries </li></ul>
  52. 56. References <ul><li>SMW Homepage: http://semantic-mediawiki.org </li></ul><ul><li>MW Templates: http://www.mediawiki.org/wiki/Help:Templates </li></ul><ul><li>SF Homepage: http://www.mediawiki.org/wiki/ Extension:Semantic_Forms </li></ul><ul><li>SMW #ask: http://semantic-mediawiki.org/wiki/ Help:Inline_queries </li></ul><ul><li>SMW demo sites: </li></ul><ul><ul><li>http://pgscdemo.referata.com </li></ul></ul><ul><ul><li>http://discoursedb.org </li></ul></ul><ul><ul><li>http://sandbox.referata.com </li></ul></ul>
  53. 57. Cell Lines Wiki
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