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  1. 1. Best of both worlds : Combining the user-friendliness of Wikis and the rigor of biological databases Sylvain Brohée Roland Barriot Yves Moreau
  2. 2. Biological databases  Databases are crucial in almost any biological research.  More and more biological databases (1170 described in NAR since 2004)  Large (Ensembl, pubmed, …)  Smaller and more specialized  Maintenance problem  abundant literature  funding comes to its end  curator leaves the lab  Solution : collaborative databases  Use of the MediaWiki engine (PHP)
  3. 3. MediaWiki advantages +  More and more biological collaborative databases are based on the MediaWiki motor (Wikiprotein, WikiPathways, ...).  Free all-in-one solution to build collaborative databases :  (Almost) no programming skills needed.  User rights (read only, edition, …) managed.  User friendly and wide spread system.
  4. 4. MediaWiki drawbacks -  All data are contained in one unique underlying database.  All pages have to be created and filled manually.  Data are not structured (free text).  Generally, biological databases are very well structured. Some consist only in a set of tables.  No possibility to include tools (blast, prioritization, …).
  5. 5. Classical wiki representation Wiki database (PostgreSQL, MySQL) Administration Wiki User rights User preferences MediaWiki Wiki configuration (PHP) website Images Articles Stats History … ext 1 ext 2
  6. 6. Mediawiki extensions  MediaWiki extensions are pieces of PHP code used to improve the existing wiki functionalities or to bring new ones.  We developed WikiOpener an extension to MediaWiki :  Easy (automated) inclusion and edition of external data  Include code in order to run tools  Automatic creation of wiki articles.
  7. 7. Wiki with WikiOpener extension Wiki database Administration User rights Wiki configuration MediaWiki Wiki Image Articles (PHP) website s Data Stats Layout … Form fields ext 2 ... Extensions WikiOpener WikiOpener components (PHP) Web DAS Flat Database ... Other data sources service track files
  8. 8. Applications CHDWiki YTPdb Congenital Heart Defects Yeast Transport Proteins http://homes.esat.kuleuven.be/~bioisuer/chdwiki http://homes.esat.kuleuven.be/~sbrohee/ytpdb
  9. 9. A typical WikiOpener page
  10. 10. A typical WikiOpener page  Structured data coming from an external relational database.  Layout is specified as a wiki page.  Automatically displayed on all pages of type (namespace) Ytpdbgene (even if it is not manually created).  Edition of structured data  Non structured text from the main database
  11. 11. WikiOpener forms
  12. 12. How does it work? A simple Bibliography example
  13. 13. How does it work? A simple Bibliography example YTPdb gene substrate Wiki database Raw text of the Bibliography article references = References = <wikiopener>getReferences|Refer ... Administration encesLayout|All </wikiopener> User rights Wiki configuration WikiOpener component getReference.p Articles Returns an array of arrays. ... Raw text of the ReferenceLayout article Bibliography References.foreach <?php ReferenceLayout *{NAME}{TITLE}{YEAR}{JOURNAL} $result = array(); References.end_foreach ... if (param[0] == “All”) { $query = “SELECT * FROM YTPDB.references”;} ... return $result; ?>
  14. 14. Conclusion  WikiOpener solves the main drawbacks of biological wikis  Display and edition of both formatted and unformatted text.  Displayed data may come come from everywhere (database, DAS track, web service).  Automatic creation of wiki pages filled with the external data.  Easy integration of code (javascript, PHP, ...) to run tools.  http://www.mediawiki.org/wiki/Extension:WikiOpener
  15. 15. Thanks  Roland Barriot  Yves Moreau  Bernard Thienpont  Jeroen Breckpot  Koen Devriendt  Bruno André