Brohee_wiki_BOSC2009
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Brohee_wiki_BOSC2009 Brohee_wiki_BOSC2009 Presentation Transcript

  • Best of both worlds : Combining the user-friendliness of Wikis and the rigor of biological databases Sylvain Brohée Roland Barriot Yves Moreau
  • 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)
  • 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.
  • 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, …).
  • 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
  • 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.
  • 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
  • Applications CHDWiki YTPdb Congenital Heart Defects Yeast Transport Proteins http://homes.esat.kuleuven.be/~bioisuer/chdwiki http://homes.esat.kuleuven.be/~sbrohee/ytpdb
  • A typical WikiOpener page
  • 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
  • WikiOpener forms
  • How does it work? A simple Bibliography example
  • 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; ?>
  • 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
  • Thanks  Roland Barriot  Yves Moreau  Bernard Thienpont  Jeroen Breckpot  Koen Devriendt  Bruno André